diff --git a/docs/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.html b/docs/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.html
index d7c3035dd..a11847dcc 100644
--- a/docs/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.html
+++ b/docs/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.html
@@ -561,7 +561,7 @@ <h2>Ecological Interactions</h2>
                 <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
                 <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
                     <title id="network-svg-title">Ecological interaction network for Model Cyanobacterial Consortia Core Microbiome</title>
-                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, mutualism, colonization facilitation).</desc>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.</desc>
                 </svg>
                 <div class="network-legend">
                     <div class="legend-item">
@@ -569,18 +569,8 @@ <h2>Ecological Interactions</h2>
                     </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolDiamond"
-                             data-color="#57c7ab"></svg> Cross-feeding
-                    </div>
-                    <div class="legend-item">
-                        <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolSquare"
-                             data-color="#9f2ebb"></svg> Mutualism
-                    </div>
-                    <div class="legend-item">
-                        <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolPlus"
-                             data-color="#edab12"></svg> Colonization facilitation
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -588,18 +578,13 @@ <h2>Ecological Interactions</h2>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>Plasmid-Mediated Cyanobacteria-Heterotroph Symbiosis</h3>
-                    <span class="interaction-type">MUTUALISM</span>
+                    <h3>Putative Plasmid Functions in the Cyanobacterial Core Microbiome</h3>
                 </div>
-                <p class="prewrap interaction-description">Core noncyanobacterial species are significantly enriched in plasmids, and plasmid-encoded functions are suggested to mediate symbiotic interactions with the cyanobacterial hosts.</p>
-
+                <p class="prewrap interaction-description">PARTIAL - Core microbiome MAGs are enriched in putative plasmid contigs carrying transport, carbohydrate-metabolism and signaling functions. Cobinning assigns plasmids to MAGs and 98% of predicted plasmids were not circularized. Their contribution to phototroph-heterotroph establishment or maintenance is HYPOTHESIZED from genomic content, not demonstrated plasmid transfer, curing, reciprocal fitness or metabolite flux.</p>
 
-                <p><strong>Source Taxon:</strong> core noncyanobacterial heterotrophs</p>
 
 
 
-                <p><strong>Target Taxon:</strong> model cyanobacterial hosts</p>
-
 
 
 
@@ -628,7 +613,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/40626910/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40626910</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - PARTIAL (IN_VITRO)
                         </div>
 
                         <div class="snippet">"core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions"</div>
@@ -642,9 +627,8 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Core Micronutrient and Anoxygenic Photosynthesis Functions</h3>
-                    <span class="interaction-type">CROSS_FEEDING</span>
                 </div>
-                <p class="prewrap interaction-description">The 25-species core microbiome is statistically enriched for micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis functions, indicating shared community-level metabolic contributions across consortia.</p>
+                <p class="prewrap interaction-description">Core microbiome MAGs are statistically enriched in micronutrient biosynthesis, membrane transport and anoxygenic photosynthesis potential; 20 of 25 core MAGs encode anoxygenic photosystem components. These are genomic capabilities. Cross-feeding of costly cofactors or cyanobacterial products is HYPOTHESIZED, not measured expression, transferred metabolites or partner-specific growth benefit.</p>
 
 
 
@@ -702,10 +686,9 @@ <h4>Evidence</h4>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>Host- and Inoculum-Independent Core Recruitment</h3>
-                    <span class="interaction-type">COLONIZATION_FACILITATION</span>
+                    <h3>Reproducible Core Recruitment Across Hosts and Inocula</h3>
                 </div>
-                <p class="prewrap interaction-description">Despite varying cyanobacterial host species and freshwater inoculum sources, the 108 consortia converged on the same noncyanobacterial core, indicating reproducible cyanobacterium-driven recruitment.</p>
+                <p class="prewrap interaction-description">Among 108 retained consortia, 25 species met an operational core definition: occurrence with at least four host strains and at least two source environments under replicated criteria. Individual core species occurred in 18.5%-68.5% of samples, not universally. Communities stabilized and showed broad convergence, while both host strain and inoculum significantly affected composition. Host-driven facilitation is PARTIAL because cyanobacteria-free controls were absent, leaving medium and laboratory selection unresolved.</p>
 
 
 
@@ -727,25 +710,23 @@ <h3>Host- and Inoculum-Independent Core Recruitment</h3>
 
 
 
-                <div class="interaction-flow">
-                    <strong>Downstream Effects:</strong>
 
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> Core Micronutrient and Anoxygenic Photosynthesis Functions
-                        <p class="prewrap causal-description">Reproducible 25-species core recruitment made it possible to statistically validate shared micronutrient-biosynthesis, metabolite- transport, and anoxygenic-photosynthesis functions in the core microbiome.</p>
-                    </div>
 
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> Plasmid-Mediated Cyanobacteria-Heterotroph Symbiosis
-                        <p class="prewrap causal-description">The recruited core species were significantly enriched in plasmids whose encoded functions suggested plasmid-mediated cyanobacteria-heterotroph symbiotic roles.</p>
-                    </div>
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
 
-                </div>
+                    <li class="evidence-item">
+                        <div>
 
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/40626910/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40626910</a>
 
+                            - SUPPORT (IN_VITRO)
+                        </div>
 
-                <h4>Evidence</h4>
-                <ul class="evidence-list">
+                        <div class="snippet">"despite host and inoculum diversity, these consortia converged on a similar set of noncyanobacterial taxa"</div>
+
+                    </li>
 
                     <li class="evidence-item">
                         <div>
@@ -756,7 +737,20 @@ <h4>Evidence</h4>
                             - SUPPORT (IN_VITRO)
                         </div>
 
-                        <div class="snippet">"despite host and inoculum diversity, these consortia converged on a similar set of noncyanobacterial taxa"</div>
+                        <div class="snippet">"Individual core species were present in 18.5%–68.5% of all samples"</div>
+
+                    </li>
+
+                    <li class="evidence-item">
+                        <div>
+
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/40626910/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40626910</a>
+
+                            - PARTIAL (IN_VITRO)
+                        </div>
+
+                        <div class="snippet">"The absence of cyanobacteria-free controls limited our ability to disentangle effects solely attributable to media or laboratory conditions."</div>
 
                     </li>
 
@@ -769,6 +763,25 @@ <h4>Evidence</h4>
 
         <!-- Associated Datasets -->
 
+        <section id="discussions">
+            <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Which selective mechanisms explain the measured community responses?
+                </h3>
+                <p class="prewrap">The primary source establishes replicated enrichment, but host/source variation persists and the authors report no cyanobacteria-free controls. Bioinformatic removal of predicted plasmid contigs is an analytical comparison, not a biological plasmid intervention. Quantify selective host, plasmid and metabolite-exchange contributions before adding mechanistic arrows; statistical analysis enabled by recruitment is not a downstream ecological cause.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Putative Plasmid Functions in the Cyanobacterial Core Microbiome</code>, <code>ecological_interactions#Core Micronutrient and Anoxygenic Photosynthesis Functions</code>, <code>ecological_interactions#Reproducible Core Recruitment Across Hosts and Inocula</code></p>
+
+
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 
@@ -1059,7 +1072,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:0";
-            var intType = "MUTUALISM";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
@@ -1072,7 +1085,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             nodes.push({
                 id: intId,
-                label: "Plasmid-Mediated Cyanobacteria-Heterotroph Symbiosis",
+                label: "Putative Plasmid Functions in the Cyanobacterial Core Microbiome",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -1081,23 +1094,13 @@ <h4 style="color: var(--text);">Evidence</h4>
             });
 
 
-            var srcKey = "core noncyanobacterial heterotrophs";
-            if (taxonNodeIds[srcKey]) {
-                links.push({ source: taxonNodeIds[srcKey], target: intId });
-            }
-
-
 
-            var tgtKey = "model cyanobacterial hosts";
-            if (taxonNodeIds[tgtKey]) {
-                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
-            }
 
         })();
 
         (function() {
             var intId = "interaction:1";
-            var intType = "CROSS_FEEDING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
@@ -1129,7 +1132,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:2";
-            var intType = "COLONIZATION_FACILITATION";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
@@ -1138,11 +1141,11 @@ <h4 style="color: var(--text);">Evidence</h4>
             processes.push("interspecies interaction between organisms");
 
 
-            var evidenceCount = 1;
+            var evidenceCount = 3;
 
             nodes.push({
                 id: intId,
-                label: "Host- and Inoculum-Independent Core Recruitment",
+                label: "Reproducible Core Recruitment Across Hosts and Inocula",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
diff --git a/docs/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.html b/docs/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.html
index 160deef4d..3acfb8d3f 100644
--- a/docs/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.html
+++ b/docs/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.html
@@ -654,7 +654,7 @@ <h2>Ecological Interactions</h2>
                 <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
                 <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
                     <title id="network-svg-title">Ecological interaction network for Model Lignocellulose Formaldehyde Cross-Feeding Community</title>
-                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (mutualism, competition, commensalism).</desc>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, competition).</desc>
                 </svg>
                 <div class="network-legend">
                     <div class="legend-item">
@@ -662,8 +662,8 @@ <h2>Ecological Interactions</h2>
                     </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolSquare"
-                             data-color="#9f2ebb"></svg> Mutualism
+                             aria-hidden="true" data-symbol="symbolDiamond"
+                             data-color="#57c7ab"></svg> Cross-feeding
                     </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
@@ -672,8 +672,8 @@ <h2>Ecological Interactions</h2>
                     </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolWye"
-                             data-color="#cf7830"></svg> Commensalism
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -682,9 +682,8 @@ <h2>Ecological Interactions</h2>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Formaldehyde Toxicity from Aromatic Breakdown</h3>
-                    <span class="interaction-type">COMPETITION</span>
                 </div>
-                <p class="prewrap interaction-description">P. putida growing on vanillic acid produces formaldehyde that can reach inhibitory concentrations for C. fimi, creating a toxic-intermediate interaction within the lignocellulose community.</p>
+                <p class="prewrap interaction-description">P. putida growing on vanillic acid accumulates approximately 0.6-0.8 mM formaldehyde, above the 0.5 mM concentration that prevents C. fimi growth in separate tolerance assays. This demonstrates toxic potential, not that the transient formaldehyde pulse is the dominant cause of coculture inhibition: P. putida also inhibits C. fimi on protocatechuic acid without formaldehyde generation.</p>
 
 
                 <p><strong>Source Taxon:</strong> Pseudomonas putida</p>
@@ -723,7 +722,7 @@ <h3>Formaldehyde Toxicity from Aromatic Breakdown</h3>
 
                     <div class="flow-item">
                         <span class="flow-arrow">→</span> Methylotrophic Formaldehyde Mitigation
-                        <p class="prewrap causal-description">Formaldehyde generated during P. putida growth on vanillic acid is the toxic intermediate that M. extorquens consumes to mitigate inhibition of C. fimi in the model lignocellulose community.</p>
+                        <p class="prewrap causal-description">P. putida vanillic-acid metabolism supplies formaldehyde that M. extorquens can consume, reducing the magnitude and duration of its accumulation. The biochemical production-to-removal link is supported; relief of C. fimi growth inhibition is PARTIAL, because inhibition persists in the formaldehyde-free PCA control and is not fully ameliorated by M. extorquens.</p>
                     </div>
 
                 </div>
@@ -766,9 +765,8 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Methylotrophic Formaldehyde Mitigation</h3>
-                    <span class="interaction-type">COMMENSALISM</span>
                 </div>
-                <p class="prewrap interaction-description">M. extorquens lowers formaldehyde concentrations generated by P. putida, mitigating toxin accumulation in the synthetic lignocellulose community.</p>
+                <p class="prewrap interaction-description">M. extorquens addition lowers measurable formaldehyde produced by P. putida. PARTIAL - C. fimi is a potential beneficiary of reduced toxin exposure, but detoxification does not completely ameliorate its growth inhibition; other interactions dominate the tested batch conditions. Neither neutral fitness of the methylotroph nor full recipient rescue is established by the concentration change.</p>
 
 
                 <p><strong>Source Taxon:</strong> Methylorubrum extorquens</p>
@@ -809,23 +807,36 @@ <h4>Evidence</h4>
 
                     </li>
 
+                    <li class="evidence-item">
+                        <div>
+
+                            <a href="https://doi.org/10.3390/microorganisms9020321"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.3390/microorganisms9020321</a>
+
+                            - SUPPORT (IN_VITRO)
+                        </div>
+
+                        <div class="snippet">"M. extorquens was not able to completely ameliorate either the formaldehyde production or the growth inhibition."</div>
+
+                    </li>
+
                 </ul>
 
             </div>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>C. fimi and M. extorquens Metabolite Exchange</h3>
-                    <span class="interaction-type">MUTUALISM</span>
+                    <h3>Conditional Methionine Rescue and C. fimi Cross-Feeding</h3>
+                    <span class="interaction-type">CROSS_FEEDING</span>
                 </div>
-                <p class="prewrap interaction-description">The system supports a possible mutualistic interaction between C. fimi and M. extorquens through metabolite exchange, including engineered methionine release by M. extorquens that supports methionine-limited C. fimi.</p>
+                <p class="prewrap interaction-description">Selected methionine-overproducing M. extorquens CM4744 supports C. fimi without supplied methionine, but only when methanol or succinate supports the producer; wild-type M. extorquens does not provide this rescue. The listed source-to-target direction denotes this methionine supply. Separately, C. fimi supports M. extorquens growth without an added methylotroph carbon substrate, consistent with reverse-direction carbon cross-feeding whose carrier was not resolved here. PARTIAL - These positive assays do not demonstrate autonomous reciprocal methionine-for-carbon codependence in one unsupplemented condition.</p>
 
 
-                <p><strong>Source Taxon:</strong> Cellulomonas fimi</p>
+                <p><strong>Source Taxon:</strong> Methylorubrum extorquens</p>
 
 
 
-                <p><strong>Target Taxon:</strong> Methylorubrum extorquens</p>
+                <p><strong>Target Taxon:</strong> Cellulomonas fimi</p>
 
 
 
@@ -863,7 +874,7 @@ <h4>Evidence</h4>
                             <a href="https://doi.org/10.3390/microorganisms9020321"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.3390/microorganisms9020321</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - PARTIAL (IN_VITRO)
                         </div>
 
                         <div class="snippet">"mutualistic interaction between C. fimi and M. extorquens through metabolite exchange"</div>
@@ -883,6 +894,19 @@ <h4>Evidence</h4>
 
                     </li>
 
+                    <li class="evidence-item">
+                        <div>
+
+                            <a href="https://doi.org/10.3390/microorganisms9020321"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.3390/microorganisms9020321</a>
+
+                            - SUPPORT (IN_VITRO)
+                        </div>
+
+                        <div class="snippet">"wild-type M. extorquens did not promote C. fimi growth."</div>
+
+                    </li>
+
                 </ul>
 
             </div>
@@ -892,7 +916,7 @@ <h4>Evidence</h4>
                     <h3>Resource Competition in Model Lignocellulose Medium</h3>
                     <span class="interaction-type">COMPETITION</span>
                 </div>
-                <p class="prewrap interaction-description">The consortium displayed resource competition and interspecies differences in growth requirements and toxin sensitivities.</p>
+                <p class="prewrap interaction-description">PARTIAL - P. putida suppresses C. fimi growth and cellobiose consumption even on formaldehyde-free protocatechuic acid. Iron and vitamin/amino-acid supplementation improves coculture growth, consistent with competition for iron or methionine and other supplements. Spent medium lowers yield, but depletion and a secreted inhibitor remain alternatives; high iron itself inhibits C. fimi. These experiments do not establish a single exclusive inhibitory resource or competition causing methionine overproduction.</p>
 
 
 
@@ -914,17 +938,6 @@ <h3>Resource Competition in Model Lignocellulose Medium</h3>
 
 
 
-                <div class="interaction-flow">
-                    <strong>Downstream Effects:</strong>
-
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> C. fimi and M. extorquens Metabolite Exchange
-                        <p class="prewrap causal-description">Competition for methionine was one inhibitory axis that could be resolved by adding an M. extorquens strain engineered to excrete methionine for C. fimi.
-</p>
-                    </div>
-
-                </div>
-
 
 
                 <h4>Evidence</h4>
@@ -936,13 +949,26 @@ <h4>Evidence</h4>
                             <a href="https://doi.org/10.3390/microorganisms9020321"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.3390/microorganisms9020321</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - PARTIAL (IN_VITRO)
                         </div>
 
                         <div class="snippet">"resource competition"</div>
 
                     </li>
 
+                    <li class="evidence-item">
+                        <div>
+
+                            <a href="https://doi.org/10.3390/microorganisms9020321"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.3390/microorganisms9020321</a>
+
+                            - PARTIAL (IN_VITRO)
+                        </div>
+
+                        <div class="snippet">"This could indicate either the effect of a soluble compound produced by P. putida, or the depletion by P. putida of important medium components, or both."</div>
+
+                    </li>
+
                 </ul>
 
             </div>
@@ -952,6 +978,25 @@ <h4>Evidence</h4>
 
         <!-- Associated Datasets -->
 
+        <section id="discussions">
+            <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Which selective mechanisms explain the measured community responses?
+                </h3>
+                <p class="prewrap">Preserve direct formaldehyde lowering, C.fimi-supported methylotroph growth and selected-overproducer methionine rescue. The PCA control retains inhibition without formaldehyde; supplementation and spent medium do not uniquely isolate resource depletion. CM4744 rescue requires additional producer substrate, while true codependence is proposed for future evolution. Remove the competition-to-engineered-exchange arrow because it encodes investigator intervention, not spontaneous biological induction.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Formaldehyde Toxicity from Aromatic Breakdown</code>, <code>ecological_interactions#Methylotrophic Formaldehyde Mitigation</code>, <code>ecological_interactions#Conditional Methionine Rescue and C. fimi Cross-Feeding</code>, <code>ecological_interactions#Resource Competition in Model Lignocellulose Medium</code></p>
+
+
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 
@@ -1319,7 +1364,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:0";
-            var intType = "COMPETITION";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
@@ -1361,7 +1406,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:1";
-            var intType = "COMMENSALISM";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
@@ -1370,7 +1415,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             var processes = [];
 
-            var evidenceCount = 1;
+            var evidenceCount = 2;
 
             nodes.push({
                 id: intId,
@@ -1399,7 +1444,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:2";
-            var intType = "MUTUALISM";
+            var intType = "CROSS_FEEDING";
             var metabolites = [];
 
 
@@ -1412,11 +1457,11 @@ <h4 style="color: var(--text);">Evidence</h4>
             processes.push("interspecies interaction between organisms");
 
 
-            var evidenceCount = 2;
+            var evidenceCount = 3;
 
             nodes.push({
                 id: intId,
-                label: "C. fimi and M. extorquens Metabolite Exchange",
+                label: "Conditional Methionine Rescue and C. fimi Cross-Feeding",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -1425,14 +1470,14 @@ <h4 style="color: var(--text);">Evidence</h4>
             });
 
 
-            var srcKey = "Cellulomonas fimi";
+            var srcKey = "Methylorubrum extorquens";
             if (taxonNodeIds[srcKey]) {
                 links.push({ source: taxonNodeIds[srcKey], target: intId });
             }
 
 
 
-            var tgtKey = "Methylorubrum extorquens";
+            var tgtKey = "Cellulomonas fimi";
             if (taxonNodeIds[tgtKey]) {
                 links.push({ source: intId, target: taxonNodeIds[tgtKey] });
             }
@@ -1450,7 +1495,7 @@ <h4 style="color: var(--text);">Evidence</h4>
             processes.push("interspecies interaction between organisms");
 
 
-            var evidenceCount = 1;
+            var evidenceCount = 2;
 
             nodes.push({
                 id: intId,
diff --git a/docs/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.html b/docs/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.html
index b2b121849..9771ab58d 100644
--- a/docs/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.html
+++ b/docs/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.html
@@ -598,7 +598,7 @@ <h2>Ecological Interactions</h2>
                 <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
                 <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
                     <title id="network-svg-title">Ecological interaction network for Moss-Microbe Complex Regolith Biofertilizer</title>
-                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (mutualism, colonization facilitation).</desc>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (colonization facilitation).</desc>
                 </svg>
                 <div class="network-legend">
                     <div class="legend-item">
@@ -606,13 +606,13 @@ <h2>Ecological Interactions</h2>
                     </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolSquare"
-                             data-color="#9f2ebb"></svg> Mutualism
+                             aria-hidden="true" data-symbol="symbolPlus"
+                             data-color="#edab12"></svg> Colonization facilitation
                     </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolPlus"
-                             data-color="#edab12"></svg> Colonization facilitation
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -623,8 +623,7 @@ <h2>Ecological Interactions</h2>
                     <h3>Moss-facilitated microbial colonization on Martian simulant</h3>
                     <span class="interaction-type">COLONIZATION_FACILITATION</span>
                 </div>
-                <p class="prewrap interaction-description">In the Martian (MGS) simulant, whose high bulk density and low porosity impeded microbial effectiveness, the moss Hypnum plumaeforme functioned as a biological buffer that facilitated colonization by the plant growth-promoting bacteria and restored plant growth responses. The moss thereby acts as a key facilitator of plant-microbe interactions under harsh regolith-simulant conditions.
-</p>
+                <p class="prewrap interaction-description">The primary abstract reports that Hypnum plumaeforme acts as a biological buffer facilitating microbial colonization in the dense, low-porosity Martian simulant, where microbial effectiveness is otherwise impeded. PARTIAL - This is the reported facilitation interpretation; abstract-only access does not resolve selective colonization mediation versus other moss-associated changes.</p>
 
 
 
@@ -651,8 +650,7 @@ <h3>Moss-facilitated microbial colonization on Martian simulant</h3>
 
                     <div class="flow-item">
                         <span class="flow-arrow">→</span> Moss-microbe co-treatment enhances barley growth and soil quality
-                        <p class="prewrap causal-description">Moss-buffered microbial colonization on the low-porosity Martian simulant restores plant growth responses in the combined moss-microbe treatment.
-</p>
+                        <p class="prewrap causal-description">PARTIAL - Moss-associated buffering and microbial colonization are reported to restore plant growth responses on the Martian simulant. This is a supported mechanistic interpretation of the combined treatment, but the available abstract does not isolate colonization from organic inputs, soil changes or other growth-promoting activities.</p>
                     </div>
 
                 </div>
@@ -695,10 +693,8 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Moss-microbe co-treatment enhances barley growth and soil quality</h3>
-                    <span class="interaction-type">MUTUALISM</span>
                 </div>
-                <p class="prewrap interaction-description">Combined application of moss and its associated bacteria (versus moss alone or microbes alone) significantly enhanced barley shoot biomass, dry weight, soil organic matter, available phosphate, and cation exchange capacity, indicating a community-level synergy of the moss-microbe complex improving plant growth and soil functionality on the simulants.
-</p>
+                <p class="prewrap interaction-description">The study compared moss alone, microbes alone and combined application on lunar and Martian simulants. The primary abstract reports significant combined-treatment improvements in barley shoot biomass, dry weight, organic matter, available phosphate and cation exchange capacity. It does not specify every endpoint comparator or demonstrate reciprocal moss-microbial fitness; these positive treatment outcomes are not classified as mutualism.</p>
 
 
 
@@ -720,17 +716,6 @@ <h3>Moss-microbe co-treatment enhances barley growth and soil quality</h3>
 
 
 
-                <div class="interaction-flow">
-                    <strong>Downstream Effects:</strong>
-
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> Moss-Microbe Rhizosphere Metabolite Accumulation
-                        <p class="prewrap causal-description">The same moss-microbe co-treatment that improved barley growth and soil quality also reprogrammed the rhizosphere metabolite profile.
-</p>
-                    </div>
-
-                </div>
-
 
 
                 <h4>Evidence</h4>
@@ -756,10 +741,8 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Moss-Microbe Rhizosphere Metabolite Accumulation</h3>
-                    <span class="interaction-type">MUTUALISM</span>
                 </div>
-                <p class="prewrap interaction-description">Metabolite profiling of the moss-microbe complex treatment revealed significant accumulation of growth-related D-ribose and D-gluconate, suggesting that the complex reprograms rhizosphere metabolism on the soil simulants.
-</p>
+                <p class="prewrap interaction-description">Metabolite profiling reports accumulation of D-ribose and D-gluconate with moss-microbe treatment. Reprogrammed rhizosphere metabolism is HYPOTHESIZED from altered pools; producer identity, interspecies transfer and the causal contribution to barley growth are not resolved by the available abstract. Growth/soil improvement and metabolite changes are parallel reported treatment outcomes, not an established causal sequence.</p>
 
 
 
@@ -820,6 +803,25 @@ <h4>Evidence</h4>
 
         <!-- Associated Datasets -->
 
+        <section id="discussions">
+            <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Which selective mechanisms explain the measured community responses?
+                </h3>
+                <p class="prewrap">The primary publisher abstract supports positive treatment effects and a colonization interpretation. Full publisher access returned403; this does not show that selective controls were absent. Obtain authorized full Methods to resolve colonization versus other moss effects, endpoint comparators and metabolite mediation. Devosia is detected rather than a selected inoculant; do not assign all measured outcomes to each bacterial member.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Moss-facilitated microbial colonization on Martian simulant</code>, <code>ecological_interactions#Moss-microbe co-treatment enhances barley growth and soil quality</code>, <code>ecological_interactions#Moss-Microbe Rhizosphere Metabolite Accumulation</code></p>
+
+
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 
@@ -995,7 +997,7 @@ <h2>Environmental Factors</h2>
 
         (function() {
             var intId = "interaction:1";
-            var intType = "MUTUALISM";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
@@ -1023,7 +1025,7 @@ <h2>Environmental Factors</h2>
 
         (function() {
             var intId = "interaction:2";
-            var intType = "MUTUALISM";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
diff --git a/docs/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.html b/docs/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.html
index d289d1756..da79815d5 100644
--- a/docs/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.html
+++ b/docs/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.html
@@ -993,7 +993,7 @@ <h2>Ecological Interactions</h2>
                 <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
                 <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
                     <title id="network-svg-title">Ecological interaction network for Mucin Glycan-Degrading MDSC Synthetic Gut Community</title>
-                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, niche partitioning).</desc>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.</desc>
                 </svg>
                 <div class="network-legend">
                     <div class="legend-item">
@@ -1001,13 +1001,8 @@ <h2>Ecological Interactions</h2>
                     </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolDiamond"
-                             data-color="#57c7ab"></svg> Cross-feeding
-                    </div>
-                    <div class="legend-item">
-                        <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolSquare2"
-                             data-color="#1212ed"></svg> Niche partitioning
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -1016,9 +1011,8 @@ <h2>Ecological Interactions</h2>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Mucin-Type-Dependent MDSC Restructuring</h3>
-                    <span class="interaction-type">NICHE_PARTITIONING</span>
                 </div>
-                <p class="prewrap interaction-description">After four sequential transfers, the MDSC stabilized into distinct species-level compositions on PGM, PGM plus BSM, and PGM plus added sialylated glycans, with BSM alone supporting limited growth.</p>
+                <p class="prewrap interaction-description">After four sequential transfers, the MDSC stabilized into distinct species-level compositions on PGM, PGM plus BSM, and PGM plus added sialylated glycans, with BSM alone supporting limited growth. Substrate-regime interventions establish composition responses, but taxon-specific niche partitioning or competition is an interpretation, not selectively isolated by these abundance data.</p>
 
 
 
@@ -1045,7 +1039,7 @@ <h3>Mucin-Type-Dependent MDSC Restructuring</h3>
 
                     <div class="flow-item">
                         <span class="flow-arrow">→</span> Substrate-Dependent Mucin Glycan Degradation
-                        <p class="prewrap causal-description">Community composition tracked with different O- and N-glycan degradation patterns on the four mucin substrate regimes.</p>
+                        <p class="prewrap causal-description">PARTIAL - Substrate-selected community composition can change the available glycan-degrading enzyme repertoire and thereby influence degradation. The paper reports coordinated composition and glycan changes, including convergence of added-glycan degradation rates, but changes mucin substrate rather than holding substrate fixed while selectively changing composition. Direct substrate accessibility and composition-mediated effects are therefore not separated.</p>
                     </div>
 
                 </div>
@@ -1075,9 +1069,8 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Substrate-Dependent Mucin Glycan Degradation</h3>
-                    <span class="interaction-type">CROSS_FEEDING</span>
                 </div>
-                <p class="prewrap interaction-description">The MDSC degraded PGM O-glycans, PGM plus BSM O-glycans, and PGM plus added sialylated glycans in sequential batch culture, but showed limited growth and only minimal O-glycan degradation when BSM was supplied alone.</p>
+                <p class="prewrap interaction-description">The MDSC rapidly degrades PGM and mixed PGM/BSM O-glycans and degrades added sialylated glycans. BSM alone supports little growth and only minimal O-glycan degradation, while its low-abundance identified N-glycans are completely degraded. Added sialylated structures show different early rates and some remain detectable at120 h. These community substrate-processing outcomes do not identify the donor-recipient fluxes implied by a pairwise cross-feeding mechanism.</p>
 
 
 
@@ -1124,9 +1117,8 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Mucin-Type-Dependent Fermentation Profile</h3>
-                    <span class="interaction-type">CROSS_FEEDING</span>
                 </div>
-                <p class="prewrap interaction-description">HPLC measurements showed that PGM, BSM, PGM/BSM, and PGM plus sialylated glycans yielded distinct extracellular metabolite profiles, including condition-dependent changes in acetate, propionate, formate, and ethanol after community stabilization.</p>
+                <p class="prewrap interaction-description">HPLC measurements showed that PGM, BSM, PGM/BSM, and PGM plus sialylated glycans yielded distinct extracellular metabolite profiles, including condition-dependent changes in acetate, propionate, formate, and ethanol after community stabilization. These are extracellular pool profiles, not measured transfer between particular members. Low metabolite output on BSM may include yeast-extract fermentation; an increase in metabolite concentration is not proof of production exclusively from mucin.</p>
 
 
 
@@ -1247,7 +1239,7 @@ <h2>Associated Datasets</h2>
         </section>
 
         <section id="discussions">
-            <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
+            <h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>
 
             <div class="discussion">
                 <h3>
@@ -1262,6 +1254,21 @@ <h3>
 
 
 
+            </div>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Which selective mechanisms explain the measured community responses?
+                </h3>
+                <p class="prewrap">Preserve the experimentally altered mucin regimes and positive composition, glycan and metabolite responses. The retained composition-to-degradation mechanism is PARTIAL because composition and substrate accessibility change together. Do not confuse failure to degrade most BSM O-glycans with failure to degrade its N-glycans, or A.muciniphila abundance with demonstrated sialic-acid utilization. Monoculture BSM plus threonine did not restore A.muciniphila growth. Existing unresolved pairwise-flux discussion and prior957/958/959 repairs remain intact.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Mucin-Type-Dependent MDSC Restructuring</code>, <code>ecological_interactions#Substrate-Dependent Mucin Glycan Degradation</code>, <code>ecological_interactions#Mucin-Type-Dependent Fermentation Profile</code></p>
+
+
+
+
             </div>
 
         </section>
@@ -1767,7 +1774,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:0";
-            var intType = "NICHE_PARTITIONING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
@@ -1795,7 +1802,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:1";
-            var intType = "CROSS_FEEDING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
@@ -1823,7 +1830,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:2";
-            var intType = "CROSS_FEEDING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
diff --git a/history/records/Model_Cyanobacterial_Consortia_Core_Microbiome/2026-10-07T024303Z-codex-050bf5.yaml b/history/records/Model_Cyanobacterial_Consortia_Core_Microbiome/2026-10-07T024303Z-codex-050bf5.yaml
new file mode 100644
index 000000000..a2fe2bfdd
--- /dev/null
+++ b/history/records/Model_Cyanobacterial_Consortia_Core_Microbiome/2026-10-07T024303Z-codex-050bf5.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml
+  slug: Model_Cyanobacterial_Consortia_Core_Microbiome
+session:
+  id: 2026-10-07T024303Z-codex-050bf5
+  timestamp: '2026-10-07T02:43:03Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1620
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain putative plasmid enrichment; symbiotic mechanism is PARTIAL, not measured
+    mutualism.; Retain genomic functional potential without asserting measured cross-feeding.;
+    Correct operational-core and host/source boundaries; remove two analytical-workflow arrows.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml
diff --git a/history/records/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community/2026-10-07T024303Z-codex-225f8a.yaml b/history/records/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community/2026-10-07T024303Z-codex-225f8a.yaml
new file mode 100644
index 000000000..07d9b4616
--- /dev/null
+++ b/history/records/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community/2026-10-07T024303Z-codex-225f8a.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml
+  slug: Model_Lignocellulose_Formaldehyde_Crossfeeding_Community
+session:
+  id: 2026-10-07T024303Z-codex-225f8a
+  timestamp: '2026-10-07T02:43:03Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1621
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain toxic potential and production-to-mitigation link, not exclusive inhibition.;
+    Retain measured formaldehyde lowering; recipient rescue remains incomplete.; Correct methionine
+    direction and preserve two condition-specific positive growth assays, not autonomous mutualism.;
+    Bound resource competition using PCA, supplement and spent-medium controls; remove engineering-workflow
+    arrow.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml
diff --git a/history/records/Moss_Microbe_Complex_Regolith_Biofertilizer/2026-10-07T024303Z-codex-ab7b96.yaml b/history/records/Moss_Microbe_Complex_Regolith_Biofertilizer/2026-10-07T024303Z-codex-ab7b96.yaml
new file mode 100644
index 000000000..52278f24d
--- /dev/null
+++ b/history/records/Moss_Microbe_Complex_Regolith_Biofertilizer/2026-10-07T024303Z-codex-ab7b96.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml
+  slug: Moss_Microbe_Complex_Regolith_Biofertilizer
+session:
+  id: 2026-10-07T024303Z-codex-ab7b96
+  timestamp: '2026-10-07T02:43:03Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1622
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain reported colonization facilitation with PARTIAL mediation arrow.; Preserve
+    treatment gains; remove unsupported reciprocal-fitness classification and shared-outcome
+    arrow.; Retain metabolite accumulation, not traced cross-feeding or demonstrated growth
+    mediation.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml
diff --git a/history/records/Mucin_Glycan_MDSC_Synthetic_Gut_Community/2026-10-07T024304Z-codex-132d35.yaml b/history/records/Mucin_Glycan_MDSC_Synthetic_Gut_Community/2026-10-07T024304Z-codex-132d35.yaml
new file mode 100644
index 000000000..bbad2f0ae
--- /dev/null
+++ b/history/records/Mucin_Glycan_MDSC_Synthetic_Gut_Community/2026-10-07T024304Z-codex-132d35.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml
+  slug: Mucin_Glycan_MDSC_Synthetic_Gut_Community
+session:
+  id: 2026-10-07T024304Z-codex-132d35
+  timestamp: '2026-10-07T02:43:04Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1623
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain causal substrate response; qualify composition-to-degradation mediation.;
+    Preserve O-glycan versus N-glycan and residual-added-glycan distinctions without claiming
+    resolved cross-feeding.; Retain measured metabolite profiles and prior analyte fix; pool
+    changes are not transfer flux.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml
diff --git a/kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml b/kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml
index 76474d139..c3847c3aa 100644
--- a/kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml
+++ b/kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml
@@ -109,22 +109,12 @@ taxonomy:
       forming a 25-species core microbiome
     explanation: Supports the recurrent core noncyanobacterial membership.
 ecological_interactions:
-- name: Plasmid-Mediated Cyanobacteria-Heterotroph Symbiosis
-  description: Core noncyanobacterial species are significantly enriched in
-    plasmids, and plasmid-encoded functions are suggested to mediate symbiotic
-    interactions with the cyanobacterial hosts.
-  interaction_type: MUTUALISM
+- name: Putative Plasmid Functions in the Cyanobacterial Core Microbiome
+  description: PARTIAL - Core microbiome MAGs are enriched in putative plasmid contigs carrying transport, carbohydrate-metabolism
+    and signaling functions. Cobinning assigns plasmids to MAGs and 98% of predicted plasmids were not circularized.
+    Their contribution to phototroph-heterotroph establishment or maintenance is HYPOTHESIZED from genomic content,
+    not demonstrated plasmid transfer, curing, reciprocal fitness or metabolite flux.
   scope: COMMUNITY_LEVEL
-  source_taxon:
-    preferred_term: core noncyanobacterial heterotrophs
-    term:
-      id: NCBITaxon:2
-      label: Bacteria
-  target_taxon:
-    preferred_term: model cyanobacterial hosts
-    term:
-      id: NCBITaxon:1117
-      label: Cyanobacteriota
   biological_processes:
   - preferred_term: interspecies interaction between organisms
     term:
@@ -132,17 +122,17 @@ ecological_interactions:
       label: biological process involved in interspecies interaction between organisms
   evidence:
   - reference: PMID:40626910
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: IN_VITRO
-    snippet: core species showed significant enrichment of plasmids, and functions
-      encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions
-    explanation: Supports plasmid-mediated symbiotic functions in the core consortium.
+    snippet: core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested
+      plasmid-mediated roles in symbiotic interactions
+    explanation: Supports plasmid enrichment and proposed symbiotic roles, not experimentally demonstrated mutual
+      benefit.
 - name: Core Micronutrient and Anoxygenic Photosynthesis Functions
-  description: The 25-species core microbiome is statistically enriched for
-    micronutrient biosynthesis, metabolite transport, and anoxygenic
-    photosynthesis functions, indicating shared community-level metabolic
-    contributions across consortia.
-  interaction_type: CROSS_FEEDING
+  description: Core microbiome MAGs are statistically enriched in micronutrient biosynthesis, membrane transport
+    and anoxygenic photosynthesis potential; 20 of 25 core MAGs encode anoxygenic photosystem components. These
+    are genomic capabilities. Cross-feeding of costly cofactors or cyanobacterial products is HYPOTHESIZED, not
+    measured expression, transferred metabolites or partner-specific growth benefit.
   scope: COMMUNITY_LEVEL
   biological_processes:
   - preferred_term: vitamin biosynthetic process
@@ -161,37 +151,39 @@ ecological_interactions:
   - reference: PMID:40626910
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: core microbiome functionalities in micronutrient biosynthesis,
-      metabolite transport, and anoxygenic photosynthesis
-    explanation: Supports the curated set of shared functional categories.
-- name: Host- and Inoculum-Independent Core Recruitment
-  description: Despite varying cyanobacterial host species and freshwater inoculum
-    sources, the 108 consortia converged on the same noncyanobacterial core,
-    indicating reproducible cyanobacterium-driven recruitment.
-  interaction_type: COLONIZATION_FACILITATION
+    snippet: core microbiome functionalities in micronutrient biosynthesis, metabolite transport, and anoxygenic
+      photosynthesis
+    explanation: Supports the functional-enrichment analysis; encoded potential does not demonstrate exchange.
+- name: Reproducible Core Recruitment Across Hosts and Inocula
+  description: 'Among 108 retained consortia, 25 species met an operational core definition: occurrence with at
+    least four host strains and at least two source environments under replicated criteria. Individual core species
+    occurred in 18.5%-68.5% of samples, not universally. Communities stabilized and showed broad convergence, while
+    both host strain and inoculum significantly affected composition. Host-driven facilitation is PARTIAL because
+    cyanobacteria-free controls were absent, leaving medium and laboratory selection unresolved.'
   scope: COMMUNITY_LEVEL
   biological_processes:
   - preferred_term: interspecies interaction between organisms
     term:
       id: GO:0044419
       label: biological process involved in interspecies interaction between organisms
-  downstream:
-  - target: Core Micronutrient and Anoxygenic Photosynthesis Functions
-    description: Reproducible 25-species core recruitment made it possible to
-      statistically validate shared micronutrient-biosynthesis, metabolite-
-      transport, and anoxygenic-photosynthesis functions in the core microbiome.
-  - target: Plasmid-Mediated Cyanobacteria-Heterotroph Symbiosis
-    description: The recruited core species were significantly enriched in plasmids
-      whose encoded functions suggested plasmid-mediated cyanobacteria-heterotroph
-      symbiotic roles.
   evidence:
   - reference: PMID:40626910
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: despite host and inoculum diversity, these consortia converged on a
-      similar set of noncyanobacterial taxa
-    explanation: Supports host- and inoculum-independent recruitment of the core
-      microbiome.
+    snippet: despite host and inoculum diversity, these consortia converged on a similar set of noncyanobacterial
+      taxa
+    explanation: Supports broad convergence across hosts and inocula, not absence of host or inoculum effects.
+  - reference: PMID:40626910
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: Individual core species were present in 18.5%–68.5% of all samples
+    explanation: Operational core membership is not universal occurrence.
+  - reference: PMID:40626910
+    supports: PARTIAL
+    evidence_source: IN_VITRO
+    snippet: The absence of cyanobacteria-free controls limited our ability to disentangle effects solely attributable
+      to media or laboratory conditions.
+    explanation: Directly states the limitation on causal host recruitment.
 environmental_factors:
 - name: Freshwater inoculum diversity
   value: three distinct freshwater sources
@@ -253,3 +245,27 @@ rare_earth_elements_present: []
 metal_relevance: NOT_APPLICABLE
 metal_notes: No metal or rare earth element processing role is curated for this
   freshwater cyanobacterium-heterotroph coculture framework.
+discussions:
+- discussion_id: core_recruitment_and_plasmid_function
+  prompt: Which selective mechanisms explain the measured community responses?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  posed_by: codex
+  posed_date: '2026-10-07'
+  rationale: The primary source establishes replicated enrichment, but host/source variation persists and the authors
+    report no cyanobacteria-free controls. Bioinformatic removal of predicted plasmid contigs is an analytical comparison,
+    not a biological plasmid intervention. Quantify selective host, plasmid and metabolite-exchange contributions
+    before adding mechanistic arrows; statistical analysis enabled by recruitment is not a downstream ecological
+    cause.
+  attaches_to:
+  - ecological_interactions#Putative Plasmid Functions in the Cyanobacterial Core Microbiome
+  - ecological_interactions#Core Micronutrient and Anoxygenic Photosynthesis Functions
+  - ecological_interactions#Reproducible Core Recruitment Across Hosts and Inocula
+curation_history:
+- timestamp: '2026-10-07T02:43:02Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: 'Retain putative plasmid enrichment; symbiotic mechanism is PARTIAL, not measured mutualism.; Retain
+    genomic functional potential without asserting measured cross-feeding.; Correct operational-core and host/source
+    boundaries; remove two analytical-workflow arrows. Issue #1620; reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml'
+  llm_assisted: true
diff --git a/kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml b/kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml
index c23236415..457ec5134 100644
--- a/kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml
+++ b/kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml
@@ -181,10 +181,10 @@ related_ingredients:
     explanation: Identifies vanillic acid as the aromatic substrate metabolized into formaldehyde.
 ecological_interactions:
 - name: Formaldehyde Toxicity from Aromatic Breakdown
-  description: P. putida growing on vanillic acid produces formaldehyde that can reach inhibitory
-    concentrations for C. fimi, creating a toxic-intermediate interaction within the lignocellulose
-    community.
-  interaction_type: COMPETITION
+  description: 'P. putida growing on vanillic acid accumulates approximately 0.6-0.8 mM formaldehyde, above the
+    0.5 mM concentration that prevents C. fimi growth in separate tolerance assays. This demonstrates toxic potential,
+    not that the transient formaldehyde pulse is the dominant cause of coculture inhibition: P. putida also inhibits
+    C. fimi on protocatechuic acid without formaldehyde generation.'
   scope: PAIRWISE
   source_taxon:
     preferred_term: Pseudomonas putida
@@ -208,9 +208,10 @@ ecological_interactions:
       label: biological process involved in interspecies interaction between organisms
   downstream:
   - target: Methylotrophic Formaldehyde Mitigation
-    description: Formaldehyde generated during P. putida growth on vanillic acid
-      is the toxic intermediate that M. extorquens consumes to mitigate
-      inhibition of C. fimi in the model lignocellulose community.
+    description: P. putida vanillic-acid metabolism supplies formaldehyde that M. extorquens can consume, reducing
+      the magnitude and duration of its accumulation. The biochemical production-to-removal link is supported; relief
+      of C. fimi growth inhibition is PARTIAL, because inhibition persists in the formaldehyde-free PCA control
+      and is not fully ameliorated by M. extorquens.
   evidence:
   - reference: doi:10.3390/microorganisms9020321
     supports: SUPPORT
@@ -223,9 +224,10 @@ ecological_interactions:
     snippet: exceed the minimum inhibitory concentration for C. fimi
     explanation: Supports formaldehyde toxicity toward C. fimi.
 - name: Methylotrophic Formaldehyde Mitigation
-  description: M. extorquens lowers formaldehyde concentrations generated by P. putida, mitigating
-    toxin accumulation in the synthetic lignocellulose community.
-  interaction_type: COMMENSALISM
+  description: M. extorquens addition lowers measurable formaldehyde produced by P. putida. PARTIAL - C. fimi is
+    a potential beneficiary of reduced toxin exposure, but detoxification does not completely ameliorate its growth
+    inhibition; other interactions dominate the tested batch conditions. Neither neutral fitness of the methylotroph
+    nor full recipient rescue is established by the concentration change.
   scope: PAIRWISE
   source_taxon:
     preferred_term: Methylorubrum extorquens
@@ -248,22 +250,31 @@ ecological_interactions:
     evidence_source: IN_VITRO
     snippet: presence of M. extorquens lowers those concentrations
     explanation: Supports methylotrophic lowering of formaldehyde concentrations.
-- name: C. fimi and M. extorquens Metabolite Exchange
-  description: The system supports a possible mutualistic interaction between C. fimi and M. extorquens
-    through metabolite exchange, including engineered methionine release by M. extorquens that supports
-    methionine-limited C. fimi.
-  interaction_type: MUTUALISM
+  - reference: doi:10.3390/microorganisms9020321
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: M. extorquens was not able to completely ameliorate either the formaldehyde production or the growth
+      inhibition.
+    explanation: Bounds detoxification without erasing the observed reduction.
+- name: Conditional Methionine Rescue and C. fimi Cross-Feeding
+  description: Selected methionine-overproducing M. extorquens CM4744 supports C. fimi without supplied methionine,
+    but only when methanol or succinate supports the producer; wild-type M. extorquens does not provide this rescue.
+    The listed source-to-target direction denotes this methionine supply. Separately, C. fimi supports M. extorquens
+    growth without an added methylotroph carbon substrate, consistent with reverse-direction carbon cross-feeding
+    whose carrier was not resolved here. PARTIAL - These positive assays do not demonstrate autonomous reciprocal
+    methionine-for-carbon codependence in one unsupplemented condition.
+  interaction_type: CROSS_FEEDING
   scope: PAIRWISE
   source_taxon:
-    preferred_term: Cellulomonas fimi
-    term:
-      id: NCBITaxon:1708
-      label: Cellulomonas fimi
-  target_taxon:
     preferred_term: Methylorubrum extorquens
     term:
       id: NCBITaxon:408
       label: Methylorubrum extorquens
+  target_taxon:
+    preferred_term: Cellulomonas fimi
+    term:
+      id: NCBITaxon:1708
+      label: Cellulomonas fimi
   metabolites:
   - preferred_term: methionine
     term:
@@ -276,18 +287,27 @@ ecological_interactions:
       label: biological process involved in interspecies interaction between organisms
   evidence:
   - reference: doi:10.3390/microorganisms9020321
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: IN_VITRO
     snippet: mutualistic interaction between C. fimi and M. extorquens through metabolite exchange
-    explanation: Supports the curated metabolite-exchange interaction.
+    explanation: The abstract explicitly proposes a possibility, not established autonomous mutualism.
   - reference: doi:10.3390/microorganisms9020321
     supports: SUPPORT
     evidence_source: IN_VITRO
     snippet: M. extorquens to support C. fimi through the production of methionine
-    explanation: Supports methionine excretion by engineered M. extorquens as a C. fimi-supporting exchange.
+    explanation: Supports the selected methionine-overproducer-to-C.fimi direction, conditional on producer growth
+      substrate.
+  - reference: doi:10.3390/microorganisms9020321
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: wild-type M. extorquens did not promote C. fimi growth.
+    explanation: Distinguishes the selected overproducer from the wild-type assay.
 - name: Resource Competition in Model Lignocellulose Medium
-  description: The consortium displayed resource competition and interspecies differences in growth
-    requirements and toxin sensitivities.
+  description: PARTIAL - P. putida suppresses C. fimi growth and cellobiose consumption even on formaldehyde-free
+    protocatechuic acid. Iron and vitamin/amino-acid supplementation improves coculture growth, consistent with
+    competition for iron or methionine and other supplements. Spent medium lowers yield, but depletion and a secreted
+    inhibitor remain alternatives; high iron itself inhibits C. fimi. These experiments do not establish a single
+    exclusive inhibitory resource or competition causing methionine overproduction.
   interaction_type: COMPETITION
   scope: COMMUNITY_LEVEL
   biological_processes:
@@ -295,18 +315,18 @@ ecological_interactions:
     term:
       id: GO:0044419
       label: biological process involved in interspecies interaction between organisms
-  downstream:
-  - target: C. fimi and M. extorquens Metabolite Exchange
-    description: >
-      Competition for methionine was one inhibitory axis that could be resolved
-      by adding an M. extorquens strain engineered to excrete methionine for C.
-      fimi.
   evidence:
   - reference: doi:10.3390/microorganisms9020321
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: IN_VITRO
     snippet: resource competition
     explanation: Supports resource competition as an ecological dynamic in the community.
+  - reference: doi:10.3390/microorganisms9020321
+    supports: PARTIAL
+    evidence_source: IN_VITRO
+    snippet: This could indicate either the effect of a soluble compound produced by P. putida, or the depletion
+      by P. putida of important medium components, or both.
+    explanation: Retains alternative inhibition mechanisms rather than certifying a single depleted resource.
 environmental_factors:
 - name: Lignocellulose-relevant polymer recalcitrance
   value: complex organic polymers such as lignocellulose
@@ -407,3 +427,29 @@ cultivation_setup:
     snippet: we used 48-well tissue culture plates (Corning Costar, Tewksbury, MA, USA)
       with a total volume of 640 µL per well, and incubated in a LPX44 Plate Hotel
       (LiCONiC, Mauren, Liechtenstein) with shaking at 650 RPM
+discussions:
+- discussion_id: formaldehyde_and_conditional_exchange_boundaries
+  prompt: Which selective mechanisms explain the measured community responses?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  posed_by: codex
+  posed_date: '2026-10-07'
+  rationale: Preserve direct formaldehyde lowering, C.fimi-supported methylotroph growth and selected-overproducer
+    methionine rescue. The PCA control retains inhibition without formaldehyde; supplementation and spent medium
+    do not uniquely isolate resource depletion. CM4744 rescue requires additional producer substrate, while true
+    codependence is proposed for future evolution. Remove the competition-to-engineered-exchange arrow because it
+    encodes investigator intervention, not spontaneous biological induction.
+  attaches_to:
+  - ecological_interactions#Formaldehyde Toxicity from Aromatic Breakdown
+  - ecological_interactions#Methylotrophic Formaldehyde Mitigation
+  - ecological_interactions#Conditional Methionine Rescue and C. fimi Cross-Feeding
+  - ecological_interactions#Resource Competition in Model Lignocellulose Medium
+curation_history:
+- timestamp: '2026-10-07T02:43:02Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: 'Retain toxic potential and production-to-mitigation link, not exclusive inhibition.; Retain measured
+    formaldehyde lowering; recipient rescue remains incomplete.; Correct methionine direction and preserve two condition-specific
+    positive growth assays, not autonomous mutualism.; Bound resource competition using PCA, supplement and spent-medium
+    controls; remove engineering-workflow arrow. Issue #1621; reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml'
+  llm_assisted: true
diff --git a/kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml b/kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml
index 5d6116462..6e257df70 100644
--- a/kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml
+++ b/kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml
@@ -153,12 +153,10 @@ taxonomy:
     explanation: Names Devosia among the genera stably present in moss-treated simulant soils.
 ecological_interactions:
 - name: Moss-facilitated microbial colonization on Martian simulant
-  description: >
-    In the Martian (MGS) simulant, whose high bulk density and low porosity impeded
-    microbial effectiveness, the moss Hypnum plumaeforme functioned as a biological
-    buffer that facilitated colonization by the plant growth-promoting bacteria and
-    restored plant growth responses. The moss thereby acts as a key facilitator of
-    plant-microbe interactions under harsh regolith-simulant conditions.
+  description: The primary abstract reports that Hypnum plumaeforme acts as a biological buffer facilitating microbial
+    colonization in the dense, low-porosity Martian simulant, where microbial effectiveness is otherwise impeded.
+    PARTIAL - This is the reported facilitation interpretation; abstract-only access does not resolve selective
+    colonization mediation versus other moss-associated changes.
   interaction_type: COLONIZATION_FACILITATION
   scope: COMMUNITY_LEVEL
   biological_processes:
@@ -168,9 +166,10 @@ ecological_interactions:
       label: biological process involved in interspecies interaction between organisms
   downstream:
   - target: Moss-microbe co-treatment enhances barley growth and soil quality
-    description: >
-      Moss-buffered microbial colonization on the low-porosity Martian simulant
-      restores plant growth responses in the combined moss-microbe treatment.
+    description: PARTIAL - Moss-associated buffering and microbial colonization are reported to restore plant growth
+      responses on the Martian simulant. This is a supported mechanistic interpretation of the combined treatment,
+      but the available abstract does not isolate colonization from organic inputs, soil changes or other growth-promoting
+      activities.
   evidence:
   - reference: doi:10.1016/j.ecolind.2025.114023
     supports: SUPPORT
@@ -180,40 +179,35 @@ ecological_interactions:
   - reference: doi:10.1016/j.ecolind.2025.114023
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: moss acts not merely as an organic input but as a key facilitator of plant–microbe interactions under harsh conditions
-    explanation: Supports the moss as a facilitator of plant-microbe interactions under harsh regolith-simulant conditions.
+    snippet: moss acts not merely as an organic input but as a key facilitator of plant–microbe interactions under
+      harsh conditions
+    explanation: Supports the moss as a facilitator of plant-microbe interactions under harsh regolith-simulant
+      conditions.
 - name: Moss-microbe co-treatment enhances barley growth and soil quality
-  description: >
-    Combined application of moss and its associated bacteria (versus moss alone or
-    microbes alone) significantly enhanced barley shoot biomass, dry weight, soil
-    organic matter, available phosphate, and cation exchange capacity, indicating a
-    community-level synergy of the moss-microbe complex improving plant growth and soil
-    functionality on the simulants.
+  description: The study compared moss alone, microbes alone and combined application on lunar and Martian simulants.
+    The primary abstract reports significant combined-treatment improvements in barley shoot biomass, dry weight,
+    organic matter, available phosphate and cation exchange capacity. It does not specify every endpoint comparator
+    or demonstrate reciprocal moss-microbial fitness; these positive treatment outcomes are not classified as mutualism.
   scope: COMMUNITY_LEVEL
-  interaction_type: MUTUALISM
   biological_processes:
   - preferred_term: biological process involved in interspecies interaction between organisms
     term:
       id: GO:0044419
       label: biological process involved in interspecies interaction between organisms
-  downstream:
-  - target: Moss-Microbe Rhizosphere Metabolite Accumulation
-    description: >
-      The same moss-microbe co-treatment that improved barley growth and soil
-      quality also reprogrammed the rhizosphere metabolite profile.
   evidence:
   - reference: doi:10.1016/j.ecolind.2025.114023
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: moss–microbe co-treatment significantly enhanced shoot biomass, dry weight, organic matter content, available phosphate, and cation exchange capacity
-    explanation: Supports the community-level synergy of moss plus microbes enhancing plant growth and soil quality.
+    snippet: moss–microbe co-treatment significantly enhanced shoot biomass, dry weight, organic matter content,
+      available phosphate, and cation exchange capacity
+    explanation: Supports positive combined-treatment outcomes; does not specify superiority over each single treatment
+      for every endpoint or reciprocal fitness.
 - name: Moss-Microbe Rhizosphere Metabolite Accumulation
-  description: >
-    Metabolite profiling of the moss-microbe complex treatment revealed significant
-    accumulation of growth-related D-ribose and D-gluconate, suggesting that the
-    complex reprograms rhizosphere metabolism on the soil simulants.
+  description: Metabolite profiling reports accumulation of D-ribose and D-gluconate with moss-microbe treatment.
+    Reprogrammed rhizosphere metabolism is HYPOTHESIZED from altered pools; producer identity, interspecies transfer
+    and the causal contribution to barley growth are not resolved by the available abstract. Growth/soil improvement
+    and metabolite changes are parallel reported treatment outcomes, not an established causal sequence.
   scope: COMMUNITY_LEVEL
-  interaction_type: MUTUALISM
   metabolites:
   - preferred_term: D-ribose
     term:
@@ -232,8 +226,10 @@ ecological_interactions:
   - reference: doi:10.1016/j.ecolind.2025.114023
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: Metabolite profiling further revealed the significant accumulation of growth-related compounds such as D-ribose and D-gluconate, suggesting that the moss–microbe complex may reprogram rhizosphere metabolism.
-    explanation: Supports moss-microbe treatment reshaping the rhizosphere metabolite pool.
+    snippet: Metabolite profiling further revealed the significant accumulation of growth-related compounds such
+      as D-ribose and D-gluconate, suggesting that the moss–microbe complex may reprogram rhizosphere metabolism.
+    explanation: Supports changed metabolite pools and the authors proposed metabolic interpretation, not demonstrated
+      transfer or mediation.
 environmental_factors:
 - name: Lunar (LHS) and Martian (MGS) soil simulants
   value: LHS and MGS soil simulants
@@ -274,3 +270,27 @@ related_ingredients:
     evidence_source: IN_VITRO
     snippet: accumulation of growth-related compounds such as D-ribose and D-gluconate
     explanation: Names D-gluconate among the accumulated growth-related rhizosphere metabolites.
+discussions:
+- discussion_id: moss_colonization_and_metabolite_mediation
+  prompt: Which selective mechanisms explain the measured community responses?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  posed_by: codex
+  posed_date: '2026-10-07'
+  rationale: The primary publisher abstract supports positive treatment effects and a colonization interpretation.
+    Full publisher access returned403; this does not show that selective controls were absent. Obtain authorized
+    full Methods to resolve colonization versus other moss effects, endpoint comparators and metabolite mediation.
+    Devosia is detected rather than a selected inoculant; do not assign all measured outcomes to each bacterial
+    member.
+  attaches_to:
+  - ecological_interactions#Moss-facilitated microbial colonization on Martian simulant
+  - ecological_interactions#Moss-microbe co-treatment enhances barley growth and soil quality
+  - ecological_interactions#Moss-Microbe Rhizosphere Metabolite Accumulation
+curation_history:
+- timestamp: '2026-10-07T02:43:02Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: 'Retain reported colonization facilitation with PARTIAL mediation arrow.; Preserve treatment gains; remove
+    unsupported reciprocal-fitness classification and shared-outcome arrow.; Retain metabolite accumulation, not
+    traced cross-feeding or demonstrated growth mediation. Issue #1622; reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml'
+  llm_assisted: true
diff --git a/kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml b/kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml
index 131b1deb0..ccba2ad1c 100644
--- a/kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml
+++ b/kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml
@@ -489,11 +489,10 @@ taxonomy:
     explanation: Names Desulfovibrio piger DSM 749T as an MDSC member.
 ecological_interactions:
 - name: Mucin-Type-Dependent MDSC Restructuring
-  description: >-
-    After four sequential transfers, the MDSC stabilized into distinct
-    species-level compositions on PGM, PGM plus BSM, and PGM plus added
-    sialylated glycans, with BSM alone supporting limited growth.
-  interaction_type: NICHE_PARTITIONING
+  description: After four sequential transfers, the MDSC stabilized into distinct species-level compositions on
+    PGM, PGM plus BSM, and PGM plus added sialylated glycans, with BSM alone supporting limited growth. Substrate-regime
+    interventions establish composition responses, but taxon-specific niche partitioning or competition is an interpretation,
+    not selectively isolated by these abundance data.
   scope: COMMUNITY_LEVEL
   biological_processes:
   - preferred_term: biological process involved in interspecies interaction
@@ -502,9 +501,11 @@ ecological_interactions:
       label: biological process involved in interspecies interaction between organisms
   downstream:
   - target: Substrate-Dependent Mucin Glycan Degradation
-    description: >-
-      Community composition tracked with different O- and N-glycan degradation
-      patterns on the four mucin substrate regimes.
+    description: PARTIAL - Substrate-selected community composition can change the available glycan-degrading enzyme
+      repertoire and thereby influence degradation. The paper reports coordinated composition and glycan changes,
+      including convergence of added-glycan degradation rates, but changes mucin substrate rather than holding substrate
+      fixed while selectively changing composition. Direct substrate accessibility and composition-mediated effects
+      are therefore not separated.
   evidence:
   - reference: PMID:42109165
     supports: SUPPORT
@@ -512,11 +513,11 @@ ecological_interactions:
     snippet: After four transfers, the composition of the community differed as a result of mucin type condition
     explanation: Supports mucin-type-dependent restructuring of the synthetic community.
 - name: Substrate-Dependent Mucin Glycan Degradation
-  description: >-
-    The MDSC degraded PGM O-glycans, PGM plus BSM O-glycans, and PGM plus
-    added sialylated glycans in sequential batch culture, but showed limited
-    growth and only minimal O-glycan degradation when BSM was supplied alone.
-  interaction_type: CROSS_FEEDING
+  description: The MDSC rapidly degrades PGM and mixed PGM/BSM O-glycans and degrades added sialylated glycans.
+    BSM alone supports little growth and only minimal O-glycan degradation, while its low-abundance identified N-glycans
+    are completely degraded. Added sialylated structures show different early rates and some remain detectable at120
+    h. These community substrate-processing outcomes do not identify the donor-recipient fluxes implied by a pairwise
+    cross-feeding mechanism.
   scope: COMMUNITY_LEVEL
   biological_processes:
   - preferred_term: carbohydrate metabolic process
@@ -528,14 +529,14 @@ ecological_interactions:
     supports: SUPPORT
     evidence_source: IN_VITRO
     snippet: Furthermore, glycan degradation and metabolite production were also affected by mucin type
-    explanation: Supports the substrate-dependent mucin glycan degradation and metabolic output of the MDSC.
+    explanation: Supports the substrate-dependent mucin glycan degradation and metabolic output of the MDSC. Community-level
+      outcome only; no resolved member-to-member exchange follows from this measurement.
 - name: Mucin-Type-Dependent Fermentation Profile
-  description: >-
-    HPLC measurements showed that PGM, BSM, PGM/BSM, and PGM plus sialylated
-    glycans yielded distinct extracellular metabolite profiles, including
-    condition-dependent changes in acetate, propionate, formate, and ethanol
-    after community stabilization.
-  interaction_type: CROSS_FEEDING
+  description: HPLC measurements showed that PGM, BSM, PGM/BSM, and PGM plus sialylated glycans yielded distinct
+    extracellular metabolite profiles, including condition-dependent changes in acetate, propionate, formate, and
+    ethanol after community stabilization. These are extracellular pool profiles, not measured transfer between
+    particular members. Low metabolite output on BSM may include yeast-extract fermentation; an increase in metabolite
+    concentration is not proof of production exclusively from mucin.
   scope: COMMUNITY_LEVEL
   metabolites:
   - preferred_term: acetate
@@ -564,7 +565,8 @@ ecological_interactions:
     supports: SUPPORT
     evidence_source: IN_VITRO
     snippet: Incubation of the MDSC with different mucin types resulted in distinct metabolite profiles
-    explanation: Supports mucin-type-dependent extracellular metabolite output.
+    explanation: Supports mucin-type-dependent extracellular metabolite output. Community-level outcome only; no
+      resolved member-to-member exchange follows from this measurement.
 environmental_factors:
 - name: Porcine gastric mucin
   value: '0.5'
@@ -731,50 +733,62 @@ metal_relevance: NOT_APPLICABLE
 metal_notes: No metal or rare earth element processing role is curated for this mucin glycan-degrading gut SynCom.
 discussions:
 - discussion_id: mucin-mdsc-pairwise-crossfeeding-resolution
-  prompt: >-
-    Which exact MDSC members acted as primary mucin glycan degraders, secondary
-    degraders, and hydrogen consumers in each mucin condition?
+  prompt: Which exact MDSC members acted as primary mucin glycan degraders, secondary degraders, and hydrogen consumers
+    in each mucin condition?
   kind: KNOWLEDGE_GAP
   status: OPEN
   attaches_to:
   - ecological_interactions
-  rationale: >-
-    The 2026 MDSC paper states that the community design included primary mucin
-    degraders, secondary degraders, and hydrogen consumers and measured
-    condition-level community composition, glycan degradation, and metabolite
-    production. Pairwise member-to-member carbon or gas fluxes in the exact
-    14-strain MDSC were not resolved from this paper alone, so this record
-    captures only community-level mucin responses.
+  rationale: The 2026 MDSC paper states that the community design included primary mucin degraders, secondary degraders,
+    and hydrogen consumers and measured condition-level community composition, glycan degradation, and metabolite
+    production. Pairwise member-to-member carbon or gas fluxes in the exact 14-strain MDSC were not resolved from
+    this paper alone, so this record captures only community-level mucin responses.
   posed_by: codex
   posed_date: '2026-09-20'
+- discussion_id: mucin_substrate_and_composition_mediation
+  prompt: Which selective mechanisms explain the measured community responses?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  posed_by: codex
+  posed_date: '2026-10-07'
+  rationale: Preserve the experimentally altered mucin regimes and positive composition, glycan and metabolite responses.
+    The retained composition-to-degradation mechanism is PARTIAL because composition and substrate accessibility
+    change together. Do not confuse failure to degrade most BSM O-glycans with failure to degrade its N-glycans,
+    or A.muciniphila abundance with demonstrated sialic-acid utilization. Monoculture BSM plus threonine did not
+    restore A.muciniphila growth. Existing unresolved pairwise-flux discussion and prior957/958/959 repairs remain
+    intact.
+  attaches_to:
+  - ecological_interactions#Mucin-Type-Dependent MDSC Restructuring
+  - ecological_interactions#Substrate-Dependent Mucin Glycan Degradation
+  - ecological_interactions#Mucin-Type-Dependent Fermentation Profile
 curation_history:
 - timestamp: '2026-09-20T10:22:27Z'
   curator: codex
   action: CREATE_RECORD
-  changes: >-
-    Created CommunityMech:000392 for the 14-member MDSC synthetic gut
-    community from PMID:42109165, including exact type-strain membership,
-    mucin-substrate sequential-batch cultivation, community-level
-    mucin-dependent composition, glycan-degradation and metabolite responses,
-    and linked ENA/Yoda datasets.
+  changes: Created CommunityMech:000392 for the 14-member MDSC synthetic gut community from PMID:42109165, including
+    exact type-strain membership, mucin-substrate sequential-batch cultivation, community-level mucin-dependent
+    composition, glycan-degradation and metabolite responses, and linked ENA/Yoda datasets.
   llm_assisted: true
 - timestamp: '2026-09-20T10:30:35Z'
   curator: codex
   action: FIX_MDSC_REVIEW_FINDINGS
-  changes: >-
-    Addressed adversarial review issues #957 and #958 by clarifying that PGM
-    plus SG was one condition with two added sialylated glycans, capturing the
-    sequential-batch change from 0.05% to 0.03% w/v combined sialylated glycans,
-    and narrowing the fermentation-profile description to result-level HPLC
-    outputs rather than the full standard list.
+  changes: 'Addressed adversarial review issues #957 and #958 by clarifying that PGM plus SG was one condition with
+    two added sialylated glycans, capturing the sequential-batch change from 0.05% to 0.03% w/v combined sialylated
+    glycans, and narrowing the fermentation-profile description to result-level HPLC outputs rather than the full
+    standard list.'
   llm_assisted: true
 - timestamp: '2026-09-20T11:01:12Z'
   curator: codex
   action: FIX_MDSC_GTDB_GROUNDINGS
-  changes: >-
-    Addressed CI issue #959 by grounding Akkermansia muciniphila, Bacteroides
-    caccae, Ruminococcus torques, and Blautia hydrogenotrophica with manual GTDB
-    R232 pins; marking Desulfovibrio piger as an ambiguous R232 split; and
-    retaining Faecalibacterium duncaniae as unresolved because R232 did not
-    resolve the current NCBI species to a majority GTDB cluster.
+  changes: 'Addressed CI issue #959 by grounding Akkermansia muciniphila, Bacteroides caccae, Ruminococcus torques,
+    and Blautia hydrogenotrophica with manual GTDB R232 pins; marking Desulfovibrio piger as an ambiguous R232 split;
+    and retaining Faecalibacterium duncaniae as unresolved because R232 did not resolve the current NCBI species
+    to a majority GTDB cluster.'
+  llm_assisted: true
+- timestamp: '2026-10-07T02:43:02Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: 'Retain causal substrate response; qualify composition-to-degradation mediation.; Preserve O-glycan versus
+    N-glycan and residual-added-glycan distinctions without claiming resolved cross-feeding.; Retain measured metabolite
+    profiles and prior analyte fix; pool changes are not transfer flux. Issue #1623; reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml'
   llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index bafff1c6e..5668c03c8 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,27 @@ source-based self-adversarial review. These records are not independent approval
 or proof that every graph is complete. The current inventory and summary distinguish
 `reviewed`, `pending` and `needs_research`.
 
+## Batch74: Enrichment, Conditional Rescue And Mucin Responses
+
+[Decisions](decisions/20261007-four-records-batch74.yaml),
+[validation](validation-20261007-batch74.json) and
+[self-adversarial review](adversarial-review-20261007-batch74.yaml) cover all
+13 existing nodes and seven original arrows. Four records are repaired;
+four analysis-workflow, engineering-workflow or shared-outcome links are removed.
+
+Positive core enrichment, formaldehyde lowering, conditional methionine rescue,
+moss treatment gains and mucin-substrate responses remain. Core membership is
+operational, not universal; gene content is not measured exchange. Methionine
+rescue has the corrected donor direction and producer-substrate requirement.
+Moss and mucin mediation remain explicitly bounded, with no new graph topology.
+
+All 21 graph quotations match existing caches: 17 also match fresh primary XML,
+and four moss quotations were visually matched to the publisher-indexed abstract.
+Moss full-text access returned 403; separate supplements and original figure
+pixels were not audited. All caches and non-graph blocks are preserved.
+Repairs #1620-#1623 await protected-main merge; metadata #1624 stays open.
+Four histories are appended. Self-review is not independent approval.
+
 ## Batch73: Nitrogen Mediation And Bioleaching Evidence
 
 [Decisions](decisions/20261007-four-records-batch73.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261007-batch74.yaml b/reports/causal_graph_review/adversarial-review-20261007-batch74.yaml
new file mode 100644
index 000000000..7abb66f6f
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261007-batch74.yaml
@@ -0,0 +1,204 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: b46d6272aa24de28b7e31995b74f7a306b387fff
+scope:
+- kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml
+- kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml
+- kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml
+- kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml
+validation_report: reports/causal_graph_review/validation-20261007-batch74.json
+findings:
+- issue: 1620
+  severity: P2
+  status: addressed_in_this_change
+  finding: Core membership, causal recruitment and putative functional inference.
+  disposition: Close only after protected-main merge.
+- issue: 1621
+  severity: P2
+  status: addressed_in_this_change
+  finding: Formaldehyde controls, conditional rescue, donor direction and engineering arrow.
+  disposition: Close only after protected-main merge.
+- issue: 1622
+  severity: P2
+  status: addressed_in_this_change
+  finding: Moss treatment comparators, shared outcomes and reciprocal fitness.
+  disposition: Close only after protected-main merge.
+- issue: 1623
+  severity: P2
+  status: addressed_in_this_change
+  finding: Mucin composition mediation and unresolved cross-feeding.
+  disposition: Close only after protected-main merge.
+- issue: 1624
+  severity: P2
+  status: unresolved_non_graph
+  finding: Core, strain and host metadata require separate reconciliation.
+  disposition: Keep OPEN after graph-repair merge.
+adversarial_checks:
+- Read all four whole records and every original node/arrow after the both-root baseline. Read three complete primary
+  main bodies, captions and embedded tables; no separate supplement, raw-data or figure-pixel audit. Moss scope
+  is primary abstract only after full access403, not evidence of absent controls.
+- Preserve108 retained cyanobacterial consortia and25 operational core species. Species occurrence18.5%-68.5% contradicts
+  universal membership. Both host and source effects are significant; authors explicitly lack cyanobacteria-free
+  controls. Repair the name, description and stale evidence explanation, not only the headline.
+- Genomic and plasmid enrichment are positive observations. Putative plasmid cobinning,98% noncircularized contigs
+  and bioinformatic removal do not prove biological plasmid dependence, metabolite exchange or reciprocal fitness.
+  Remove analytical-workflow edges without deleting observed nodes.
+- Retain formaldehyde generation0.6-0.8mM, C.fimi inhibition threshold0.5mM, and experimentally reduced accumulation
+  with M.extorquens. The formaldehyde-free PCA control still inhibits C.fimi; do not claim detoxification completely
+  restores growth or dominates inhibition.
+- Preserve two positive exchange results under their actual conditions. Selected CM4744 supports C.fimi without
+  supplied methionine only with added methanol/succinate; wild type does not. Separately C.fimi supports methylotroph
+  growth. Correct methionine donor direction; no claim of autonomous mutual codependence.
+- Iron/supplement rescue and spent-medium inhibition support multiple mechanisms, not an exclusive depleted resource.
+  Remove competition-to-engineered-exchange arrow because investigator selection is not biological induction of
+  overproduction. No new reverse edge or separate node added.
+- Moss primary abstract supports reported colonization facilitation, growth/soil gains and altered metabolite pools.
+  Preserve positive results while bounding endpoint comparators and colonization mediation. Shared-treatment outcomes
+  do not establish growth causing metabolite accumulation; joint application is not measured reciprocal fitness.
+- Mucin substrate changes directly affect composition, degradation and fermentation profiles. Retain composition-to-degradation
+  as PARTIAL mechanism, not a composition-only intervention. Preserve BSM O-glycan limitation versus N-glycan degradation,
+  residual added glycans and yeast-extract contribution. Do not infer A.muciniphila sialic-acid utilization from
+  enrichment.
+- Preserve existing MDSC pairwise-flux discussion and closed957/958/959 repairs. No taxonomy, strain identifier
+  or non-graph change. Metadata1624 separately tracks remaining whole-record scope; no synthetic member-specific
+  arrows invented.
+- Adversarial diff review found a remaining host-independent evidence explanation. Corrected before commit, added
+  explicit regression coverage and retained17 superseded outputs, then reran all affected and corpus gates. No stale
+  pre-fix pass is presented as final verification.
+- All13 nodes and7 original arrows have decisions;3 remain,4 noncausal links removed. All456 other records,920 caches
+  and raw non-graph blocks verified unchanged. Four append-only record/history events. Structural defects zero;44
+  baseline warnings unchanged, connectivity census unchanged.
+- Actual schema, strict, terms, references, snippets, history, both-root inventory/network/rank, repeat renders,
+  regression and lint results retained with digests. Exact descriptions parsed across456 pages, not browser screenshots.
+  Postcommit docs-current remains a separate publication gate.
+- Dedup scanned906 all-state issue titles/bodies and31 ignored/hidden local matches with explicit git/docs/site/cache
+  exclusions; prior957/958/959 fixes inspected. No exhaustive PR-comment audit or global source-absence claim. Repair1620-1623
+  stays OPEN until protected-main merge;1624 stays OPEN afterward.
+- No new causal topology and no paid provider submission. Existing denied/pending scoped authorizations unchanged.
+  Self-adversarial COMMENT is not independent approval and does not certify corpus completion.
+verification:
+  combined_regressions: 662 passed in 202.52s (0:03:22)
+  new_regression_tests: 7
+  schema_strict_terms_history: Passed with actual outputs/digests
+  references: All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks.
+    All21 graph quotations match selected caches;17 automatically match fresh primary XML and4 moss quotations were
+    visually checked against the publisher-indexed primary abstract. Cache matching is not entailment. Full moss
+    access403; all920 caches unchanged, not recertified. Prior batch73 gallium non-graph reference exception remains
+    outside this batch.
+  snippet_counts_by_record:
+    kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml:
+      MATCH: 13
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+    kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml:
+      MATCH: 26
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+    kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml:
+      MATCH: 12
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+    kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml:
+      MATCH: 28
+      RENDERING: 2
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+  primary_graph_snippet_proof:
+    automatically_primary_matched: 17
+    publisher_abstract_visual_matches: 4
+    new_nodes_or_arrows: 0
+    complete_primary_main_texts_read: 3
+    separate_supplements_or_original_figure_pixels_inspected: false
+  network:
+    existing_findings_preserved: 44
+    added_findings: {}
+    removed_findings: {}
+    interpretation: All44 baseline warnings preserved exactly. Community scope remains aggregate, not resolved member-specific
+      activity. No taxonomy or auditor-rule changes.
+  black_ruff_diff: passed
+  tested_file_sha256:
+    reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml: 4d975cf5114b018229e3fc8408b87ea6b43e50d5e40569c564aeefa4daffa8ca
+    tests/test_causal_review_batch74.py: 46f1cbe401d385001730f356bb6349965b3452c00c0f88f7b714d62f2b0c2cff
+    kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml: c995dcaed8253c17933f5cc48404f8a09438eb99dc975df2d717a08c24a69023
+    kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml: 1cdf5aaf167042938bdbdd8d9bcb0abaa322a0a4a99a7f05abd8b2658740e82c
+    kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml: 40f12b8a0f6ef7d64390819dd8c67282e465da6d24d5098d19080088dd04199d
+    kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml: 4ef5925538ded3549c72fd84eaa0786922b4f9565de33946289104cef18a5d49
+    reports/causal_graph_review/README.md: e8279363f25533e6b67b674def497791a94daea1f4c0219c7ac961ce72542a05
+  unchanged_caches: 920
+  unchanged_records: 456
+  edison:
+    required_for_this_repair: false
+    provider_submissions: 0
+    credits_spent: 0
+    rationale: Existing topology repaired; no new causal structure. Prior denied/pending scoped authorizations unchanged.
+  post_commit_docs_current: Separate publication gate, not asserted before commit.
+participant_census:
+  measurements:
+    baseline:
+      records: 460
+      with_community_level: 393
+      mixed: 125
+      community_level_only: 268
+      taxa: 1511
+      credited_solely_by_the_rule: 1240
+    current:
+      records: 460
+      with_community_level: 393
+      mixed: 125
+      community_level_only: 268
+      taxa: 1511
+      credited_solely_by_the_rule: 1240
+  delta:
+    records: 0
+    with_community_level: 0
+    mixed: 0
+    community_level_only: 0
+    taxa: 0
+    credited_solely_by_the_rule: 0
+  interpretation: No scope-count change, taxonomy edit, or auditor-rule change. Removing group-level directional
+    taxa does not establish member-resolved activity.
+corpus:
+  records: 460
+  nodes: 1447
+  edges: 620
+  review_status_counts:
+    needs_research: 25
+    pending: 196
+    reviewed: 239
+limitations:
+- Baseline before paper research covered460 records and920 caches, including both roots and ignored/hidden YAML.
+  All13 existing nodes reviewed and retained;7 original arrows become3 after removing4 noncausal workflow/shared-outcome
+  links. No new nodes/arrows or paid provider calls.
+- Full primary main bodies, embedded tables and captions read for cyanobacteria, lignocellulose and mucin. Separate
+  supplements, raw data and original figure pixels were not audited. Moss publisher full access403; publisher-indexed
+  primary abstract visually checked, not full Methods. Abstract-only access is not proof no controls exist.
+- All21 graph quotations match selected existing caches;17 also match fresh primary XML with whitespace-only normalization
+  and4 moss quotations visually match the publisher-indexed abstract. Cache matching is not entailment. No complete
+  primary articles added to the repository; all920 caches preserved.
+- Core microbiome is operational, not universal or independent of host/inoculum; plasmid content and genomic function
+  support hypotheses, not measured exchange or fitness. Preserve positive replicated enrichment and stabilization.
+- Preserve formaldehyde lowering and positive growth assays; PCA control retains inhibition. Selected CM4744 methionine
+  rescue requires added producer substrate, and C.fimi-supported methylotroph growth is a separate assay. Canonical
+  species IDs preserved; strain metadata remains separate.
+- Preserve moss treatment gains and reported facilitation. Remove shared-outcome direction and reciprocal-fitness
+  labels, not positive growth. Retain mucin substrate effects, conditional composition mediation, O/N-glycan distinction
+  and measured profiles without inferred donor-recipient flux.
+- Scanned906 all-state issue titles/bodies for dedup with31 ignored/hidden local matches under explicit git/docs/site/cache
+  exclusions. Prior957/958/959 fixes retained;1093 is unrelated cache maintenance, not a duplicate. No exhaustive
+  historical PR-comment audit or global source-absence claim.
+- All raw non-graph blocks and456 other records preserved, not recertified. Metadata1624 remains OPEN after graph
+  repair. Repair1620-1623 remain OPEN until protected-main merge. Self-adversarial COMMENT is not independent approval.
+  The whole corpus is unfinished.
diff --git a/reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml b/reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml
new file mode 100644
index 000000000..c632d7880
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml
@@ -0,0 +1,505 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: b46d6272aa24de28b7e31995b74f7a306b387fff
+baseline_commit: b46d6272aa24de28b7e31995b74f7a306b387fff
+base_tree: 31c6bbcfe3e24737b3f4e5291d8ed1235e53160e
+pre_source_baseline_sha256: 4fcf62f971101ea8197a4ac264f71e48d70b28fd2d219aa478d0f310f83d4eb9
+issues:
+- 1620
+- 1621
+- 1622
+- 1623
+unresolved_non_graph_issues:
+- 1624
+unresolved_research_issues: []
+issue_deduplication:
+  all_state_issue_titles_and_bodies: 906
+  ignored_hidden_local_search: true
+  matching_local_files: 31
+  matching_issues:
+  - 1093
+  - 959
+  - 958
+  - 957
+primary_artifacts:
+  /private/tmp/communitymech-batch74/baseline.json: 4fcf62f971101ea8197a4ac264f71e48d70b28fd2d219aa478d0f310f83d4eb9
+  /private/tmp/communitymech-batch74/cyanobacteria-metadata.json: a30ed96596030facfd2665b0075e12b2f366d0c4298a061df1dfc3c15df80c50
+  /private/tmp/communitymech-batch74/cyanobacteria-primary.txt: de09c8612dfc9428c7dbdd4e91689e8fd54d9e10023c22513bf57f7adc2d7f32
+  /private/tmp/communitymech-batch74/cyanobacteria-primary.xml: d82ce2de2afa9ff51da61455fdd2bebd6f6422610b1a06a655e04cba47504dd9
+  /private/tmp/communitymech-batch74/issue-matches.json: 0e3aecfee303560a04a302b38e6ab32464a5b637846de59cea6fbed751a2f98e
+  /private/tmp/communitymech-batch74/lignocellulose-metadata.json: 1b81e729c0f63f16284c1bfca29582eeb1f4127a5d3353aaacdb1368cf50f35f
+  /private/tmp/communitymech-batch74/lignocellulose-primary.txt: cc656b23348ad3f1f9b95b1643c541b100266b03b2725fd3c1798d07135c3124
+  /private/tmp/communitymech-batch74/lignocellulose-primary.xml: 9069f8368a141e4acc92553ce4ee25cc053f17b02bb71309b95a51a3c442c7ea
+  /private/tmp/communitymech-batch74/mucin-metadata.json: 3b0fa960f713204b88dc36d20c5aa97830fdeea369c19e4bc144d89c016de2de
+  /private/tmp/communitymech-batch74/mucin-primary.txt: 16874be4a038a16a34cac0b11d079c1162fb9028d3dd60afe0d59ccf65b6e39e
+  /private/tmp/communitymech-batch74/mucin-primary.xml: dbbd242f1536d37ff6e6fe0a57f5ab318d4f75c433f1a66951ba6ee4d6ed43c2
+  /private/tmp/communitymech-batch74/primary-manifest.json: 07268fc559f6806ddea24a1c9199ba41a76ae9388e292f73cad7b3a6e834b62c
+primary_urls:
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12368963/fullTextXML
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7914493/fullTextXML
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13158910/fullTextXML
+- https://doi.org/10.1016/j.ecolind.2025.114023
+primary_graph_snippet_count: 21
+cache_matched_graph_snippet_count: 21
+snippet_checks:
+- record: Model_Cyanobacterial_Consortia_Core_Microbiome
+  node: Putative Plasmid Functions in the Cyanobacterial Core Microbiome
+  reference: PMID:40626910
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Model_Cyanobacterial_Consortia_Core_Microbiome
+  node: Core Micronutrient and Anoxygenic Photosynthesis Functions
+  reference: PMID:40626910
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Model_Cyanobacterial_Consortia_Core_Microbiome
+  node: Reproducible Core Recruitment Across Hosts and Inocula
+  reference: PMID:40626910
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Model_Cyanobacterial_Consortia_Core_Microbiome
+  node: Reproducible Core Recruitment Across Hosts and Inocula
+  reference: PMID:40626910
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Model_Cyanobacterial_Consortia_Core_Microbiome
+  node: Reproducible Core Recruitment Across Hosts and Inocula
+  reference: PMID:40626910
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Model_Lignocellulose_Formaldehyde_Crossfeeding_Community
+  node: Formaldehyde Toxicity from Aromatic Breakdown
+  reference: doi:10.3390/microorganisms9020321
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Model_Lignocellulose_Formaldehyde_Crossfeeding_Community
+  node: Formaldehyde Toxicity from Aromatic Breakdown
+  reference: doi:10.3390/microorganisms9020321
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Model_Lignocellulose_Formaldehyde_Crossfeeding_Community
+  node: Methylotrophic Formaldehyde Mitigation
+  reference: doi:10.3390/microorganisms9020321
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Model_Lignocellulose_Formaldehyde_Crossfeeding_Community
+  node: Methylotrophic Formaldehyde Mitigation
+  reference: doi:10.3390/microorganisms9020321
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Model_Lignocellulose_Formaldehyde_Crossfeeding_Community
+  node: Conditional Methionine Rescue and C. fimi Cross-Feeding
+  reference: doi:10.3390/microorganisms9020321
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Model_Lignocellulose_Formaldehyde_Crossfeeding_Community
+  node: Conditional Methionine Rescue and C. fimi Cross-Feeding
+  reference: doi:10.3390/microorganisms9020321
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Model_Lignocellulose_Formaldehyde_Crossfeeding_Community
+  node: Conditional Methionine Rescue and C. fimi Cross-Feeding
+  reference: doi:10.3390/microorganisms9020321
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Model_Lignocellulose_Formaldehyde_Crossfeeding_Community
+  node: Resource Competition in Model Lignocellulose Medium
+  reference: doi:10.3390/microorganisms9020321
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Model_Lignocellulose_Formaldehyde_Crossfeeding_Community
+  node: Resource Competition in Model Lignocellulose Medium
+  reference: doi:10.3390/microorganisms9020321
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Moss_Microbe_Complex_Regolith_Biofertilizer
+  node: Moss-facilitated microbial colonization on Martian simulant
+  reference: doi:10.1016/j.ecolind.2025.114023
+  cache_matched: true
+  independent_primary_match: true
+  method: Existing abstract quotation visually matched to publisher-indexed primary abstract; full access403
+- record: Moss_Microbe_Complex_Regolith_Biofertilizer
+  node: Moss-facilitated microbial colonization on Martian simulant
+  reference: doi:10.1016/j.ecolind.2025.114023
+  cache_matched: true
+  independent_primary_match: true
+  method: Existing abstract quotation visually matched to publisher-indexed primary abstract; full access403
+- record: Moss_Microbe_Complex_Regolith_Biofertilizer
+  node: Moss-microbe co-treatment enhances barley growth and soil quality
+  reference: doi:10.1016/j.ecolind.2025.114023
+  cache_matched: true
+  independent_primary_match: true
+  method: Existing abstract quotation visually matched to publisher-indexed primary abstract; full access403
+- record: Moss_Microbe_Complex_Regolith_Biofertilizer
+  node: Moss-Microbe Rhizosphere Metabolite Accumulation
+  reference: doi:10.1016/j.ecolind.2025.114023
+  cache_matched: true
+  independent_primary_match: true
+  method: Existing abstract quotation visually matched to publisher-indexed primary abstract; full access403
+- record: Mucin_Glycan_MDSC_Synthetic_Gut_Community
+  node: Mucin-Type-Dependent MDSC Restructuring
+  reference: PMID:42109165
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Mucin_Glycan_MDSC_Synthetic_Gut_Community
+  node: Substrate-Dependent Mucin Glycan Degradation
+  reference: PMID:42109165
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+- record: Mucin_Glycan_MDSC_Synthetic_Gut_Community
+  node: Mucin-Type-Dependent Fermentation Profile
+  reference: PMID:42109165
+  cache_matched: true
+  independent_primary_match: true
+  method: Fresh primary XML, whitespace-only comparison
+edison:
+  required_for_this_repair: false
+  provider_submissions: 0
+  credits_spent: 0
+  rationale: Existing topology repaired; no new causal structure. Prior denied/pending scoped authorizations unchanged.
+limitations:
+- Baseline before paper research covered460 records and920 caches, including both roots and ignored/hidden YAML.
+  All13 existing nodes reviewed and retained;7 original arrows become3 after removing4 noncausal workflow/shared-outcome
+  links. No new nodes/arrows or paid provider calls.
+- Full primary main bodies, embedded tables and captions read for cyanobacteria, lignocellulose and mucin. Separate
+  supplements, raw data and original figure pixels were not audited. Moss publisher full access403; publisher-indexed
+  primary abstract visually checked, not full Methods. Abstract-only access is not proof no controls exist.
+- All21 graph quotations match selected existing caches;17 also match fresh primary XML with whitespace-only normalization
+  and4 moss quotations visually match the publisher-indexed abstract. Cache matching is not entailment. No complete
+  primary articles added to the repository; all920 caches preserved.
+- Core microbiome is operational, not universal or independent of host/inoculum; plasmid content and genomic function
+  support hypotheses, not measured exchange or fitness. Preserve positive replicated enrichment and stabilization.
+- Preserve formaldehyde lowering and positive growth assays; PCA control retains inhibition. Selected CM4744 methionine
+  rescue requires added producer substrate, and C.fimi-supported methylotroph growth is a separate assay. Canonical
+  species IDs preserved; strain metadata remains separate.
+- Preserve moss treatment gains and reported facilitation. Remove shared-outcome direction and reciprocal-fitness
+  labels, not positive growth. Retain mucin substrate effects, conditional composition mediation, O/N-glycan distinction
+  and measured profiles without inferred donor-recipient flux.
+- Scanned906 all-state issue titles/bodies for dedup with31 ignored/hidden local matches under explicit git/docs/site/cache
+  exclusions. Prior957/958/959 fixes retained;1093 is unrelated cache maintenance, not a duplicate. No exhaustive
+  historical PR-comment audit or global source-absence claim.
+- All raw non-graph blocks and456 other records preserved, not recertified. Metadata1624 remains OPEN after graph
+  repair. Repair1620-1623 remain OPEN until protected-main merge. Self-adversarial COMMENT is not independent approval.
+  The whole corpus is unfinished.
+records:
+- path: kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml
+  id: CommunityMech:000214
+  original_sha256: c49de615a48a456b57c25abccb8a6af18ba866c346437058031d25dbcec1c97a
+  record_sha256: c995dcaed8253c17933f5cc48404f8a09438eb99dc975df2d717a08c24a69023
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml
+  scope: Whole record and every existing node/arrow; bounded causal review, not whole-record certification or exhaustive
+    extension.
+  summary: Retain putative plasmid enrichment; symbiotic mechanism is PARTIAL, not measured mutualism.; Retain genomic
+    functional potential without asserting measured cross-feeding.; Correct operational-core and host/source boundaries;
+    remove two analytical-workflow arrows.
+  renamed_nodes:
+    Plasmid-Mediated Cyanobacteria-Heterotroph Symbiosis: Putative Plasmid Functions in the Cyanobacterial Core
+      Microbiome
+    Host- and Inoculum-Independent Core Recruitment: Reproducible Core Recruitment Across Hosts and Inocula
+  node_decisions:
+  - node: Putative Plasmid Functions in the Cyanobacterial Core Microbiome
+    original_node: Plasmid-Mediated Cyanobacteria-Heterotroph Symbiosis
+    rationale: Retain putative plasmid enrichment; symbiotic mechanism is PARTIAL, not measured mutualism.
+  - node: Core Micronutrient and Anoxygenic Photosynthesis Functions
+    original_node: Core Micronutrient and Anoxygenic Photosynthesis Functions
+    rationale: Retain genomic functional potential without asserting measured cross-feeding.
+  - node: Reproducible Core Recruitment Across Hosts and Inocula
+    original_node: Host- and Inoculum-Independent Core Recruitment
+    rationale: Correct operational-core and host/source boundaries; remove two analytical-workflow arrows.
+  removed_node_decisions: []
+  edges_before:
+  - source: Host- and Inoculum-Independent Core Recruitment
+    target: Core Micronutrient and Anoxygenic Photosynthesis Functions
+    description: Reproducible 25-species core recruitment made it possible to statistically validate shared micronutrient-biosynthesis,
+      metabolite- transport, and anoxygenic-photosynthesis functions in the core microbiome.
+  - source: Host- and Inoculum-Independent Core Recruitment
+    target: Plasmid-Mediated Cyanobacteria-Heterotroph Symbiosis
+    description: The recruited core species were significantly enriched in plasmids whose encoded functions suggested
+      plasmid-mediated cyanobacteria-heterotroph symbiotic roles.
+  edges_after: []
+  retained_edge_decisions: []
+  removed_edge_decisions:
+  - source: Host- and Inoculum-Independent Core Recruitment
+    target: Core Micronutrient and Anoxygenic Photosynthesis Functions
+    description: Reproducible 25-species core recruitment made it possible to statistically validate shared micronutrient-biosynthesis,
+      metabolite- transport, and anoxygenic-photosynthesis functions in the core microbiome.
+    rationale: Removed noncausal analysis/engineering workflow or shared-treatment outcome link; see node rationale
+      and issue.
+  - source: Host- and Inoculum-Independent Core Recruitment
+    target: Plasmid-Mediated Cyanobacteria-Heterotroph Symbiosis
+    description: The recruited core species were significantly enriched in plasmids whose encoded functions suggested
+      plasmid-mediated cyanobacteria-heterotroph symbiotic roles.
+    rationale: Removed noncausal analysis/engineering workflow or shared-treatment outcome link; see node rationale
+      and issue.
+  references:
+  - PMID:40626910
+  issues:
+  - 1620
+  - 1624
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Model_Cyanobacterial_Consortia_Core_Microbiome/2026-10-07T024303Z-codex-050bf5.yaml
+  source_review:
+    PMID:40626910:
+      url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12368963/fullTextXML
+      scope: Primary abstract and complete main body, embedded tables and captions; not separate supplements, raw
+        data or original figure pixels.
+- path: kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml
+  id: CommunityMech:000178
+  original_sha256: 6d6a5de1e606304c55b97639d797228890a844ef5fced1853a621965e0576d29
+  record_sha256: 1cdf5aaf167042938bdbdd8d9bcb0abaa322a0a4a99a7f05abd8b2658740e82c
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml
+  scope: Whole record and every existing node/arrow; bounded causal review, not whole-record certification or exhaustive
+    extension.
+  summary: Retain toxic potential and production-to-mitigation link, not exclusive inhibition.; Retain measured
+    formaldehyde lowering; recipient rescue remains incomplete.; Correct methionine direction and preserve two condition-specific
+    positive growth assays, not autonomous mutualism.; Bound resource competition using PCA, supplement and spent-medium
+    controls; remove engineering-workflow arrow.
+  renamed_nodes:
+    C. fimi and M. extorquens Metabolite Exchange: Conditional Methionine Rescue and C. fimi Cross-Feeding
+  node_decisions:
+  - node: Formaldehyde Toxicity from Aromatic Breakdown
+    original_node: Formaldehyde Toxicity from Aromatic Breakdown
+    rationale: Retain toxic potential and production-to-mitigation link, not exclusive inhibition.
+  - node: Methylotrophic Formaldehyde Mitigation
+    original_node: Methylotrophic Formaldehyde Mitigation
+    rationale: Retain measured formaldehyde lowering; recipient rescue remains incomplete.
+  - node: Conditional Methionine Rescue and C. fimi Cross-Feeding
+    original_node: C. fimi and M. extorquens Metabolite Exchange
+    rationale: Correct methionine direction and preserve two condition-specific positive growth assays, not autonomous
+      mutualism.
+  - node: Resource Competition in Model Lignocellulose Medium
+    original_node: Resource Competition in Model Lignocellulose Medium
+    rationale: Bound resource competition using PCA, supplement and spent-medium controls; remove engineering-workflow
+      arrow.
+  removed_node_decisions: []
+  edges_before:
+  - source: Formaldehyde Toxicity from Aromatic Breakdown
+    target: Methylotrophic Formaldehyde Mitigation
+    description: Formaldehyde generated during P. putida growth on vanillic acid is the toxic intermediate that
+      M. extorquens consumes to mitigate inhibition of C. fimi in the model lignocellulose community.
+  - source: Resource Competition in Model Lignocellulose Medium
+    target: C. fimi and M. extorquens Metabolite Exchange
+    description: 'Competition for methionine was one inhibitory axis that could be resolved by adding an M. extorquens
+      strain engineered to excrete methionine for C. fimi.
+
+      '
+  edges_after:
+  - source: Formaldehyde Toxicity from Aromatic Breakdown
+    target: Methylotrophic Formaldehyde Mitigation
+    description: P. putida vanillic-acid metabolism supplies formaldehyde that M. extorquens can consume, reducing
+      the magnitude and duration of its accumulation. The biochemical production-to-removal link is supported; relief
+      of C. fimi growth inhibition is PARTIAL, because inhibition persists in the formaldehyde-free PCA control
+      and is not fully ameliorated by M. extorquens.
+  retained_edge_decisions:
+  - source: Formaldehyde Toxicity from Aromatic Breakdown
+    target: Methylotrophic Formaldehyde Mitigation
+    description: P. putida vanillic-acid metabolism supplies formaldehyde that M. extorquens can consume, reducing
+      the magnitude and duration of its accumulation. The biochemical production-to-removal link is supported; relief
+      of C. fimi growth inhibition is PARTIAL, because inhibition persists in the formaldehyde-free PCA control
+      and is not fully ameliorated by M. extorquens.
+    rationale: P. putida vanillic-acid metabolism supplies formaldehyde that M. extorquens can consume, reducing
+      the magnitude and duration of its accumulation. The biochemical production-to-removal link is supported; relief
+      of C. fimi growth inhibition is PARTIAL, because inhibition persists in the formaldehyde-free PCA control
+      and is not fully ameliorated by M. extorquens.
+  removed_edge_decisions:
+  - source: Resource Competition in Model Lignocellulose Medium
+    target: C. fimi and M. extorquens Metabolite Exchange
+    description: 'Competition for methionine was one inhibitory axis that could be resolved by adding an M. extorquens
+      strain engineered to excrete methionine for C. fimi.
+
+      '
+    rationale: Removed noncausal analysis/engineering workflow or shared-treatment outcome link; see node rationale
+      and issue.
+  references:
+  - doi:10.3390/microorganisms9020321
+  issues:
+  - 1621
+  - 1624
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community/2026-10-07T024303Z-codex-225f8a.yaml
+  source_review:
+    doi:10.3390/microorganisms9020321:
+      url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7914493/fullTextXML
+      scope: Primary abstract and complete main body, embedded tables and captions; not separate supplements, raw
+        data or original figure pixels.
+- path: kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml
+  id: CommunityMech:000310
+  original_sha256: b2e7b2706ceac734515ae05501686a46f3d8416ff8fdfc9aee06d2f353ad70c7
+  record_sha256: 40f12b8a0f6ef7d64390819dd8c67282e465da6d24d5098d19080088dd04199d
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml
+  scope: Whole record and every existing node/arrow; bounded causal review, not whole-record certification or exhaustive
+    extension.
+  summary: Retain reported colonization facilitation with PARTIAL mediation arrow.; Preserve treatment gains; remove
+    unsupported reciprocal-fitness classification and shared-outcome arrow.; Retain metabolite accumulation, not
+    traced cross-feeding or demonstrated growth mediation.
+  renamed_nodes: {}
+  node_decisions:
+  - node: Moss-facilitated microbial colonization on Martian simulant
+    original_node: Moss-facilitated microbial colonization on Martian simulant
+    rationale: Retain reported colonization facilitation with PARTIAL mediation arrow.
+  - node: Moss-microbe co-treatment enhances barley growth and soil quality
+    original_node: Moss-microbe co-treatment enhances barley growth and soil quality
+    rationale: Preserve treatment gains; remove unsupported reciprocal-fitness classification and shared-outcome
+      arrow.
+  - node: Moss-Microbe Rhizosphere Metabolite Accumulation
+    original_node: Moss-Microbe Rhizosphere Metabolite Accumulation
+    rationale: Retain metabolite accumulation, not traced cross-feeding or demonstrated growth mediation.
+  removed_node_decisions: []
+  edges_before:
+  - source: Moss-facilitated microbial colonization on Martian simulant
+    target: Moss-microbe co-treatment enhances barley growth and soil quality
+    description: 'Moss-buffered microbial colonization on the low-porosity Martian simulant restores plant growth
+      responses in the combined moss-microbe treatment.
+
+      '
+  - source: Moss-microbe co-treatment enhances barley growth and soil quality
+    target: Moss-Microbe Rhizosphere Metabolite Accumulation
+    description: 'The same moss-microbe co-treatment that improved barley growth and soil quality also reprogrammed
+      the rhizosphere metabolite profile.
+
+      '
+  edges_after:
+  - source: Moss-facilitated microbial colonization on Martian simulant
+    target: Moss-microbe co-treatment enhances barley growth and soil quality
+    description: PARTIAL - Moss-associated buffering and microbial colonization are reported to restore plant growth
+      responses on the Martian simulant. This is a supported mechanistic interpretation of the combined treatment,
+      but the available abstract does not isolate colonization from organic inputs, soil changes or other growth-promoting
+      activities.
+  retained_edge_decisions:
+  - source: Moss-facilitated microbial colonization on Martian simulant
+    target: Moss-microbe co-treatment enhances barley growth and soil quality
+    description: PARTIAL - Moss-associated buffering and microbial colonization are reported to restore plant growth
+      responses on the Martian simulant. This is a supported mechanistic interpretation of the combined treatment,
+      but the available abstract does not isolate colonization from organic inputs, soil changes or other growth-promoting
+      activities.
+    rationale: PARTIAL - Moss-associated buffering and microbial colonization are reported to restore plant growth
+      responses on the Martian simulant. This is a supported mechanistic interpretation of the combined treatment,
+      but the available abstract does not isolate colonization from organic inputs, soil changes or other growth-promoting
+      activities.
+  removed_edge_decisions:
+  - source: Moss-microbe co-treatment enhances barley growth and soil quality
+    target: Moss-Microbe Rhizosphere Metabolite Accumulation
+    description: 'The same moss-microbe co-treatment that improved barley growth and soil quality also reprogrammed
+      the rhizosphere metabolite profile.
+
+      '
+    rationale: Removed noncausal analysis/engineering workflow or shared-treatment outcome link; see node rationale
+      and issue.
+  references:
+  - doi:10.1016/j.ecolind.2025.114023
+  issues:
+  - 1622
+  - 1624
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Moss_Microbe_Complex_Regolith_Biofertilizer/2026-10-07T024303Z-codex-ab7b96.yaml
+  source_review:
+    doi:10.1016/j.ecolind.2025.114023:
+      url: https://www.sciencedirect.com/science/article/pii/S1470160X25009550
+      scope: Primary publisher-indexed abstract only; full access403. No inference that controls are absent.
+- path: kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml
+  id: CommunityMech:000392
+  original_sha256: f9c333902ca32c15ae68dafe78ee1c56bd927329298fa2f2fc33cf9cabaf2dca
+  record_sha256: 4ef5925538ded3549c72fd84eaa0786922b4f9565de33946289104cef18a5d49
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml
+  scope: Whole record and every existing node/arrow; bounded causal review, not whole-record certification or exhaustive
+    extension.
+  summary: Retain causal substrate response; qualify composition-to-degradation mediation.; Preserve O-glycan versus
+    N-glycan and residual-added-glycan distinctions without claiming resolved cross-feeding.; Retain measured metabolite
+    profiles and prior analyte fix; pool changes are not transfer flux.
+  renamed_nodes: {}
+  node_decisions:
+  - node: Mucin-Type-Dependent MDSC Restructuring
+    original_node: Mucin-Type-Dependent MDSC Restructuring
+    rationale: Retain causal substrate response; qualify composition-to-degradation mediation.
+  - node: Substrate-Dependent Mucin Glycan Degradation
+    original_node: Substrate-Dependent Mucin Glycan Degradation
+    rationale: Preserve O-glycan versus N-glycan and residual-added-glycan distinctions without claiming resolved
+      cross-feeding.
+  - node: Mucin-Type-Dependent Fermentation Profile
+    original_node: Mucin-Type-Dependent Fermentation Profile
+    rationale: Retain measured metabolite profiles and prior analyte fix; pool changes are not transfer flux.
+  removed_node_decisions: []
+  edges_before:
+  - source: Mucin-Type-Dependent MDSC Restructuring
+    target: Substrate-Dependent Mucin Glycan Degradation
+    description: Community composition tracked with different O- and N-glycan degradation patterns on the four mucin
+      substrate regimes.
+  edges_after:
+  - source: Mucin-Type-Dependent MDSC Restructuring
+    target: Substrate-Dependent Mucin Glycan Degradation
+    description: PARTIAL - Substrate-selected community composition can change the available glycan-degrading enzyme
+      repertoire and thereby influence degradation. The paper reports coordinated composition and glycan changes,
+      including convergence of added-glycan degradation rates, but changes mucin substrate rather than holding substrate
+      fixed while selectively changing composition. Direct substrate accessibility and composition-mediated effects
+      are therefore not separated.
+  retained_edge_decisions:
+  - source: Mucin-Type-Dependent MDSC Restructuring
+    target: Substrate-Dependent Mucin Glycan Degradation
+    description: PARTIAL - Substrate-selected community composition can change the available glycan-degrading enzyme
+      repertoire and thereby influence degradation. The paper reports coordinated composition and glycan changes,
+      including convergence of added-glycan degradation rates, but changes mucin substrate rather than holding substrate
+      fixed while selectively changing composition. Direct substrate accessibility and composition-mediated effects
+      are therefore not separated.
+    rationale: PARTIAL - Substrate-selected community composition can change the available glycan-degrading enzyme
+      repertoire and thereby influence degradation. The paper reports coordinated composition and glycan changes,
+      including convergence of added-glycan degradation rates, but changes mucin substrate rather than holding substrate
+      fixed while selectively changing composition. Direct substrate accessibility and composition-mediated effects
+      are therefore not separated.
+  removed_edge_decisions: []
+  references:
+  - PMID:42109165
+  issues:
+  - 1623
+  - 1624
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Mucin_Glycan_MDSC_Synthetic_Gut_Community/2026-10-07T024304Z-codex-132d35.yaml
+  source_review:
+    PMID:42109165:
+      url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13158910/fullTextXML
+      scope: Primary abstract and complete main body, embedded tables and captions; not separate supplements, raw
+        data or original figure pixels.
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 76a4da9fc..9257d4b68 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -259,10 +259,10 @@ kb/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.yaml	CommunityMec
 kb/communities/Microhabitat_Mineral_Fungal_Bacterial_SOM_SynCom.yaml	CommunityMech:000407	5de3bf29957c111122030447d4062e79fe6a2f241f7e1ab2e213fb240d1f8b77	1	0	50.0	reports/causal_graph_review/decisions/20261007-four-records-batch73.yaml	reviewed
 kb/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.yaml	CommunityMech:000111	dbf02fa1c11105ba4622df78e4eb555143c05be77ba8abc843173ecae45994c5	3	2	90.0	reports/causal_graph_review/decisions/20261007-four-records-batch73.yaml	reviewed
 kb/communities/Mixed_Gallium_LED_Recovery_Consortium.yaml	CommunityMech:000045	c9e9c9642b62987399daa4d82a3778b14f9cbb794085e7eb8d0dd562eb4dc117	4	3	90.0	reports/causal_graph_review/decisions/20261007-four-records-batch73.yaml	needs_research
-kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml	CommunityMech:000214	c49de615a48a456b57c25abccb8a6af18ba866c346437058031d25dbcec1c97a	3	2	100.0		pending
-kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml	CommunityMech:000178	6d6a5de1e606304c55b97639d797228890a844ef5fced1853a621965e0576d29	4	2	100.0		pending
-kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml	CommunityMech:000310	b2e7b2706ceac734515ae05501686a46f3d8416ff8fdfc9aee06d2f353ad70c7	3	2	100.0		pending
-kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml	CommunityMech:000392	f9c333902ca32c15ae68dafe78ee1c56bd927329298fa2f2fc33cf9cabaf2dca	3	1	90.0		pending
+kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml	CommunityMech:000214	c995dcaed8253c17933f5cc48404f8a09438eb99dc975df2d717a08c24a69023	3	0	65.0	reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml	reviewed
+kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml	CommunityMech:000178	1cdf5aaf167042938bdbdd8d9bcb0abaa322a0a4a99a7f05abd8b2658740e82c	4	1	85.0	reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml	reviewed
+kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml	CommunityMech:000310	40f12b8a0f6ef7d64390819dd8c67282e465da6d24d5098d19080088dd04199d	3	1	83.3	reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml	reviewed
+kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml	CommunityMech:000392	4ef5925538ded3549c72fd84eaa0786922b4f9565de33946289104cef18a5d49	3	1	80.0	reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml	reviewed
 kb/communities/Mulberry_Distillers_Grains_Feed_Consortium.yaml	CommunityMech:000435	db5dd094bbd49fba2952851b1d8394c3b30d04cb08440f850ae04cc77614137d	2	0	60.0		pending
 kb/communities/Multi_stage_Anaerobic_Digestion_SynCom_YSJ_and_SynCom_J.yaml	CommunityMech:000274	bcdd603fa53d67a36c12ce282fe44becb052db2aaa44b437442efdd41004fddd	3	2	100.0		pending
 kb/communities/Multiomics_Corn_Straw_Degradation_SynCom.yaml	CommunityMech:000119	f26fcecaf12917372e9f746f0950f17599befb4a2021d770d9a823b45dc383f3	4	3	100.0		pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 86a91342b..831877216 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -3,13 +3,13 @@
   "semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.",
   "records": 460,
   "nodes": 1447,
-  "edges": 624,
+  "edges": 620,
   "records_without_nodes": 8,
-  "records_without_edges": 163,
+  "records_without_edges": 164,
   "review_status_counts": {
     "needs_research": 25,
-    "pending": 200,
-    "reviewed": 235
+    "pending": 196,
+    "reviewed": 239
   },
   "structural_defects": [],
   "network_audit": [
diff --git a/reports/causal_graph_review/validation-20261007-batch74.json b/reports/causal_graph_review/validation-20261007-batch74.json
new file mode 100644
index 000000000..48d9db933
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261007-batch74.json
@@ -0,0 +1,1369 @@
+{
+  "base_commit": "b46d6272aa24de28b7e31995b74f7a306b387fff",
+  "scope": [
+    "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml",
+    "kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml",
+    "kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml",
+    "kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml"
+  ],
+  "reference_validator_version": "0.1.7",
+  "results": [
+    {
+      "check": "Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch74/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-strict.tsv",
+        "kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-strict.log",
+      "log_sha256": "16aaa6c7168014a32de60d49191caa711815928f542bee2a994d9061275ae708",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch74/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n  files scanned:      1\n  files with ERROR:   0\n  total ERROR rows:   0\n  TSV:                /private/tmp/communitymech-batch74/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-strict.tsv\n"
+    },
+    {
+      "check": "Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-references.log",
+      "log_sha256": "4c1087a18fd3c5a42b3ea3d31a4644195e19cdc4a0314663028fed92f8e706e7",
+      "output_tail": "Validating kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n",
+      "explained_output_tail": "Validating kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n"
+    },
+    {
+      "check": "Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-snippets.log",
+      "log_sha256": "1125ff0dde8c88267205b8aa843a32ef58e84b65fee929f651c20facd8785df0",
+      "output_tail": "# 26 evidence snippets scanned across 1 files\n  MATCH      26\n  RENDERING  0\n  ASSEMBLED  0\n  WEAK       0\n  MISMATCH   0\n  NOCONTENT  0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+    },
+    {
+      "check": "Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-rank.log",
+      "log_sha256": "fe0bb95ecd7e531f617deba4bdab854b4410a2b304950c24f194becd8d9ed795",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000178\",\n    \"name\": \"Model Lignocellulose Formaldehyde Cross-Feeding Community\",\n    \"score\": 85.0,\n    \"taxonomy\": 4,\n    \"connected_taxa\": 4,\n    \"disconnected_taxa\": 0,\n    \"ecological_interactions\": 4,\n    \"downstream_edges\": 1,\n    \"interaction_evidence\": 9,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"additional_downstream\",\n      \"interaction_type\"\n    ],\n    \"path\": \"kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community/2026-10-07T024303Z-codex-225f8a.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community-history-0.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Moss_Microbe_Complex_Regolith_Biofertilizer-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Moss_Microbe_Complex_Regolith_Biofertilizer-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Moss_Microbe_Complex_Regolith_Biofertilizer-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch74/Moss_Microbe_Complex_Regolith_Biofertilizer-strict.tsv",
+        "kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Moss_Microbe_Complex_Regolith_Biofertilizer-strict.log",
+      "log_sha256": "38e3038d1b10490a7e53de29969c3d59480741a3cb8620a0e8f6457225e954ad",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch74/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n  files scanned:      1\n  files with ERROR:   0\n  total ERROR rows:   0\n  TSV:                /private/tmp/communitymech-batch74/Moss_Microbe_Complex_Regolith_Biofertilizer-strict.tsv\n"
+    },
+    {
+      "check": "Moss_Microbe_Complex_Regolith_Biofertilizer-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Moss_Microbe_Complex_Regolith_Biofertilizer-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Moss_Microbe_Complex_Regolith_Biofertilizer-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Moss_Microbe_Complex_Regolith_Biofertilizer-references.log",
+      "log_sha256": "a443b1ebd8ad7f86a0dcdf7096814bd6209589467f03652a44d299896c07ee35",
+      "output_tail": "Validating kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n",
+      "explained_output_tail": "Validating kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n"
+    },
+    {
+      "check": "Moss_Microbe_Complex_Regolith_Biofertilizer-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Moss_Microbe_Complex_Regolith_Biofertilizer-snippets.log",
+      "log_sha256": "389f1d2b093a1648cf407d53853e429a283f80eed2628a1a14cf1f38649ca780",
+      "output_tail": "# 12 evidence snippets scanned across 1 files\n  MATCH      12\n  RENDERING  0\n  ASSEMBLED  0\n  WEAK       0\n  MISMATCH   0\n  NOCONTENT  0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+    },
+    {
+      "check": "Moss_Microbe_Complex_Regolith_Biofertilizer-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Moss_Microbe_Complex_Regolith_Biofertilizer-rank.log",
+      "log_sha256": "f299df18dd7beb894ae88a09ef9e01ae099c74b50332be1c05f5eda2a37a3eae",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000310\",\n    \"name\": \"Moss-Microbe Complex Regolith Biofertilizer\",\n    \"score\": 83.3,\n    \"taxonomy\": 3,\n    \"connected_taxa\": 3,\n    \"disconnected_taxa\": 0,\n    \"ecological_interactions\": 3,\n    \"downstream_edges\": 1,\n    \"interaction_evidence\": 4,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"additional_downstream\",\n      \"interaction_type\"\n    ],\n    \"path\": \"kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Moss_Microbe_Complex_Regolith_Biofertilizer-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Moss_Microbe_Complex_Regolith_Biofertilizer/2026-10-07T024303Z-codex-ab7b96.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Moss_Microbe_Complex_Regolith_Biofertilizer-history-0.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Mucin_Glycan_MDSC_Synthetic_Gut_Community-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Mucin_Glycan_MDSC_Synthetic_Gut_Community-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Mucin_Glycan_MDSC_Synthetic_Gut_Community-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch74/Mucin_Glycan_MDSC_Synthetic_Gut_Community-strict.tsv",
+        "kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Mucin_Glycan_MDSC_Synthetic_Gut_Community-strict.log",
+      "log_sha256": "6d4d97b2cbdff69e570acbbf802b466b606f6967e292a68b7800f5197872021a",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch74/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n  files scanned:      1\n  files with ERROR:   0\n  total ERROR rows:   0\n  TSV:                /private/tmp/communitymech-batch74/Mucin_Glycan_MDSC_Synthetic_Gut_Community-strict.tsv\n"
+    },
+    {
+      "check": "Mucin_Glycan_MDSC_Synthetic_Gut_Community-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Mucin_Glycan_MDSC_Synthetic_Gut_Community-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Mucin_Glycan_MDSC_Synthetic_Gut_Community-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Mucin_Glycan_MDSC_Synthetic_Gut_Community-references.log",
+      "log_sha256": "bd5d3a158dc9dd8e4aa3c620a874dda00680b3ba9b812fb31b9f9df10748d3ef",
+      "output_tail": "Validating kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n",
+      "explained_output_tail": "Validating kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n"
+    },
+    {
+      "check": "Mucin_Glycan_MDSC_Synthetic_Gut_Community-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Mucin_Glycan_MDSC_Synthetic_Gut_Community-snippets.log",
+      "log_sha256": "d86917a18bdb9e1b11354979173a899b6230dfebe190bee96f5640fd21fc49b8",
+      "output_tail": "# 30 evidence snippets scanned across 1 files\n  MATCH      28\n  RENDERING  2\n  ASSEMBLED  0\n  WEAK       0\n  MISMATCH   0\n  NOCONTENT  0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n   2  kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+    },
+    {
+      "check": "Mucin_Glycan_MDSC_Synthetic_Gut_Community-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Mucin_Glycan_MDSC_Synthetic_Gut_Community-rank.log",
+      "log_sha256": "7e8c38b87601305ef84b24a54205879348a2d64f1267b7d43fc02758ab3e1652",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000392\",\n    \"name\": \"Mucin Glycan-Degrading MDSC Synthetic Gut Community\",\n    \"score\": 80.0,\n    \"taxonomy\": 14,\n    \"connected_taxa\": 14,\n    \"disconnected_taxa\": 0,\n    \"ecological_interactions\": 3,\n    \"downstream_edges\": 1,\n    \"interaction_evidence\": 3,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"additional_downstream\",\n      \"interaction_type\"\n    ],\n    \"path\": \"kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Mucin_Glycan_MDSC_Synthetic_Gut_Community-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Mucin_Glycan_MDSC_Synthetic_Gut_Community/2026-10-07T024304Z-codex-132d35.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Mucin_Glycan_MDSC_Synthetic_Gut_Community-history-0.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Cyanobacterial_Consortia_Core_Microbiome-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch74/Model_Cyanobacterial_Consortia_Core_Microbiome-strict.tsv",
+        "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Cyanobacterial_Consortia_Core_Microbiome-strict.log",
+      "log_sha256": "d122334b9eecc0be3f02fc6a3e6c7380489f61413b9b51990adc3dbe8877ce8e",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch74/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n  files scanned:      1\n  files with ERROR:   0\n  total ERROR rows:   0\n  TSV:                /private/tmp/communitymech-batch74/Model_Cyanobacterial_Consortia_Core_Microbiome-strict.tsv\n"
+    },
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Cyanobacterial_Consortia_Core_Microbiome-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Cyanobacterial_Consortia_Core_Microbiome-references.log",
+      "log_sha256": "baaef0ba58fee1ad13f98e141c5b119927d2adace60f760d6e4e6899182b126b",
+      "output_tail": "Validating kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n",
+      "explained_output_tail": "Validating kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n"
+    },
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Cyanobacterial_Consortia_Core_Microbiome-snippets.log",
+      "log_sha256": "6fd22c7b42f139e3b66a27210ad3d8968c80af940879c7074184305812838cca",
+      "output_tail": "# 13 evidence snippets scanned across 1 files\n  MATCH      13\n  RENDERING  0\n  ASSEMBLED  0\n  WEAK       0\n  MISMATCH   0\n  NOCONTENT  0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+    },
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Cyanobacterial_Consortia_Core_Microbiome-rank.log",
+      "log_sha256": "d4967c1f7a67ba038a16c10b0a628f947cad26e9c18a183687fee0f8abc588bb",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000214\",\n    \"name\": \"Model Cyanobacterial Consortia Core Microbiome\",\n    \"score\": 65.0,\n    \"taxonomy\": 2,\n    \"connected_taxa\": 2,\n    \"disconnected_taxa\": 0,\n    \"ecological_interactions\": 3,\n    \"downstream_edges\": 0,\n    \"interaction_evidence\": 5,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"downstream\",\n      \"interaction_type\"\n    ],\n    \"path\": \"kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Model_Cyanobacterial_Consortia_Core_Microbiome/2026-10-07T024303Z-codex-050bf5.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/Model_Cyanobacterial_Consortia_Core_Microbiome-history-0.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "inventory",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "reports/causal_graph_review/build_inventory.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/inventory.log",
+      "log_sha256": "d78844fedfeacef329e7769b6dfe380bfb85d72476204febf7c2d2398c65f102",
+      "output_tail": "{\n  \"scope\": \"Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.\",\n  \"semantic_review_rule\": \"Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.\",\n  \"records\": 460,\n  \"nodes\": 1447,\n  \"edges\": 620,\n  \"records_without_nodes\": 8,\n  \"records_without_edges\": 164,\n  \"review_status_counts\": {\n    \"needs_research\": 25,\n    \"pending\": 196,\n    \"reviewed\": 239\n  },\n  \"structural_defects\": []\n}\n"
+    },
+    {
+      "check": "network",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "communitymech.cli",
+        "audit-network",
+        "--json"
+      ],
+      "exit_code": 1,
+      "expected_exit_codes": [
+        1
+      ],
+      "log": "/private/tmp/communitymech-batch74/network.log",
+      "log_sha256": "dcb33d46aa53f5e1dec55b1cd6463b83d3723e2ebf8c97999c93d0a5f4a2fed1",
+      "output_tail": "{\n          \"preferred_term\": \"Legionella MAGs\",\n          \"term\": {\n            \"id\": \"NCBITaxon:445\",\n            \"label\": \"Legionella\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The study detected Legionella-affiliated MAGs and used them in a virulence-gene risk assessment; the source did not assert pathogenicity for a cultured Legionella isolate.\\n\"\n        },\n        \"abundance_value\": \"Lower-abundance Legionella-affiliated MAGs detected during metagenomic risk assessment.\\n\",\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:41457319\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"COMPUTATIONAL\",\n            \"snippet\": \"detection of waterborne pathogens from the Legionella genus\",\n            \"explanation\": \"Supports Legionella-affiliated lower-abundance bins as monitored biosafety-relevant members of the consortium.\\n\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Legionella MAGs' has no interactions\"\n    }\n  ],\n  \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n    {\n      \"type\": \"UNKNOWN_TARGET\",\n      \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n      \"interaction_index\": 0,\n      \"taxon\": \"Sclerotinia sclerotiorum\",\n      \"severity\": \"warning\",\n      \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n    },\n    {\n      \"type\": \"UNKNOWN_TARGET\",\n      \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n      \"interaction_index\": 1,\n      \"taxon\": \"Sclerotinia sclerotiorum\",\n      \"severity\": \"warning\",\n      \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n    }\n  ],\n  \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Acinetobacter radioresistens 50V1\",\n      \"taxon_id\": \"NCBITaxon:40216\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n          \"term\": {\n            \"id\": \"NCBITaxon:40216\",\n            \"label\": \"Acinetobacter radioresistens\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"50V1\",\n          \"genome_accession\": \"GCA_002834555.1\"\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n            \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n      \"taxon_id\": \"NCBITaxon:1270\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n          \"term\": {\n            \"id\": \"NCBITaxon:1270\",\n            \"label\": \"Micrococcus luteus\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"W4-Al-K1\",\n          \"genome_accession\": \"GCA_057816565.1\"\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n            \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n      \"taxon_id\": \"NCBITaxon:64702\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n          \"term\": {\n            \"id\": \"NCBITaxon:64702\",\n            \"label\": \"Propionibacterium cyclohexanicum\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"TA-12T\",\n          \"genome_accession\": \"GCA_900111365\",\n          \"culture_collections\": [\n            {\n              \"collection\": \"DSM\",\n              \"accession\": \"16859\"\n            }\n          ]\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n            \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n      \"taxon_id\": \"NCBITaxon:219572\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n          \"term\": {\n            \"id\": \"NCBITaxon:219572\",\n            \"label\": \"Pseudomonas antarctica\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"CMS 35T\",\n          \"genome_accession\": \"GCA_010634845\",\n          \"culture_collections\": [\n            {\n              \"collection\": \"DSM\",\n              \"accession\": \"15318\"\n            }\n          ]\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n            \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n      \"taxon_id\": \"NCBITaxon:29388\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n          \"term\": {\n            \"id\": \"NCBITaxon:29388\",\n            \"label\": \"Staphylococcus capitis\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"K1-2-2-23\",\n          \"genome_accession\": \"GCA_025272695\",\n          \"culture_collections\": [\n            {\n              \"collection\": \"DSM\",\n              \"accession\": \"111179\"\n            }\n          ]\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n            \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Streptococcus halotolerans HTS9T\",\n      \"taxon_id\": \"NCBITaxon:1814128\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n          \"term\": {\n            \"id\": \"NCBITaxon:1814128\",\n            \"label\": \"Streptococcus halotolerans\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"HTS9T\",\n          \"genome_accession\": \"GCA_001598035\",\n          \"culture_collections\": [\n            {\n              \"collection\": \"DSM\",\n              \"accession\": \"101996\"\n            }\n          ]\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n            \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n    }\n  ]\n}\n"
+    },
+    {
+      "check": "rank-all",
+      "command": [
+        "just",
+        "rank-causal-graphs"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/rank-all.log",
+      "log_sha256": "4c582286e34af3cd9d52a0aaf978ab1178bf0f007fb9731ed24962da695ec88a",
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Coculture\t2\t2\t0\t4\t2\t8\t\t0\t0\n421\t100.0\tkb/communities/Synechococcus_Saccharomyces_SPC.yaml\tCommunityMech:000067\tSynechococcus-Saccharomyces Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n422\t100.0\tkb/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml\tCommunityMech:000211\tSynechococcus-Shewanella D-Lactate Biophotovoltaic Consortium\t2\t2\t0\t3\t2\t6\t\t0\t0\n423\t100.0\tkb/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml\tCommunityMech:000149\tSynthetic Lichen Synechococcus-Rhodotorula Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n424\t100.0\tkb/communities/Syntrophobacter_Methanobacterium_Syntrophy.yaml\tCommunityMech:000068\tSyntrophobacter-Methanobacterium Syntrophic Consortium\t2\t2\t0\t3\t3\t8\t\t0\t0\n425\t100.0\tkb/communities/Syntrophobacter_Methanospirillum_Syntrophy.yaml\tCommunityMech:000069\tSyntrophobacter-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t5\t\t0\t0\n426\t100.0\tkb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml\tCommunityMech:000189\tSyntrophomonas-Methanococcus Butyrate Growth Coordination Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n427\t100.0\tkb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\tCommunityMech:000070\tSyntrophomonas-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n428\t100.0\tkb/communities/Syntrophus_Benzoate_Degrader.yaml\tCommunityMech:000071\tSyntrophus Benzoate Degrader\t2\t2\t0\t3\t2\t6\t\t0\t0\n429\t100.0\tkb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml\tCommunityMech:000187\tSyntrophus-Methanospirillum Gentianae Benzoate Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n430\t100.0\tkb/communities/THOR_Rhizosphere_Model_Community.yaml\tCommunityMech:000079\tTHOR Rhizosphere Model Community\t3\t3\t0\t4\t2\t5\t\t0\t0\n431\t100.0\tkb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml\tCommunityMech:000072\tTYQ1 Nematode Biocontrol SynCom\t8\t8\t0\t4\t4\t4\t\t0\t0\n432\t100.0\tkb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml\tCommunityMech:000100\tTeosinte-Derived Maize Biofertilizer SynCom7\t4\t4\t0\t6\t2\t12\t\t0\t0\n433\t100.0\tkb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml\tCommunityMech:000259\tThalassiosira-Marinobacter Marine Snow Coculture\t2\t2\t0\t4\t2\t10\t\t0\t0\n434\t100.0\tkb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml\tCommunityMech:000162\tThalassiosira-Ruegeria Phycosphere Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n435\t100.0\tkb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml\tCommunityMech:000182\tThermacetogenium-Methanothermobacter Acetate Oxidation 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Community\t6\t6\t0\t5\t3\t6\t\t0\t0\n441\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n442\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n443\t100.0\tkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n444\t100.0\tkb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\tCommunityMech:000188\tTrichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture\t3\t3\t0\t3\t2\t6\t\t0\t0\n445\t100.0\tkb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml\tCommunityMech:000205\tTrichoderma-E. coli Cellulosic Isobutanol Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n446\t100.0\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t3\t\t0\t0\n447\t100.0\tkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml\tCommunityMech:000270\tTrichoderma-Streptomyces Filamentous Cellulose Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n448\t100.0\tkb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml\tCommunityMech:000147\tTrichodesmium-Alteromonas Marine Consortium\t3\t3\t0\t3\t2\t5\t\t0\t0\n449\t100.0\tkb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+    },
+    {
+      "check": "render",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "communitymech.render"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/render.log",
+      "log_sha256": "d8d9ef6f5ca625c004d6aa2bf19f5a34605d27d6ead44ce0c31bc2461a121834",
+      "output_tail": "sm.html\n  \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Bacillus_SPC.html\n  \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Ecoli_SPC.html\n  \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n  \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n  \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Saccharomyces_SPC.html\n  \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n  \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n  \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n  \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n  \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n  \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n  \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophus_Benzoate_Degrader.html\n  \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n  \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n  \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/THOR_Rhizosphere_Model_Community.html\n  \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n  \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n  \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n  \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n  \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n  \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n  \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n  \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n  \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n  \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n  \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n  \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tinto_River_Iron_Cycling_Community.html\n  \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n  \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tomato_Oxylipin_SynCom3.html\n  \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n  \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n  \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n  \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichoderma_Lactate_Platform.html\n  \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n  \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n  \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n  \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Urine_Nitrification_SynCom.html\n  \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n  \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n  \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n  \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n  \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n  \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_Consortium_C1.html\n  \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_Consortium_C6.html\n  \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n  \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n  \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n  \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n  \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n  \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n  \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n  \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n  \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n  \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n  \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n  \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n  \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/hCom2_Complex_Gut_Microbiome.html\n  \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch74/docs/communities\n  \u2713 Generated browser at /private/tmp/communitymech-causal-batch74/docs/browser.html\n  \u2713 Generated landing at /private/tmp/communitymech-causal-batch74/docs/index.html\n"
+    },
+    {
+      "check": "render-repeat",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "communitymech.render"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/render-repeat.log",
+      "log_sha256": "d8d9ef6f5ca625c004d6aa2bf19f5a34605d27d6ead44ce0c31bc2461a121834",
+      "output_tail": "sm.html\n  \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Bacillus_SPC.html\n  \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Ecoli_SPC.html\n  \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n  \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n  \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Saccharomyces_SPC.html\n  \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n  \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n  \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n  \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n  \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n  \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n  \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophus_Benzoate_Degrader.html\n  \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n  \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n  \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/THOR_Rhizosphere_Model_Community.html\n  \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n  \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n  \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n  \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n  \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n  \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n  \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n  \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n  \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n  \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n  \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n  \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tinto_River_Iron_Cycling_Community.html\n  \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n  \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tomato_Oxylipin_SynCom3.html\n  \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n  \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n  \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n  \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichoderma_Lactate_Platform.html\n  \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n  \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n  \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n  \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Urine_Nitrification_SynCom.html\n  \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n  \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n  \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n  \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n  \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n  \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_Consortium_C1.html\n  \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_Consortium_C6.html\n  \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n  \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n  \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n  \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n  \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n  \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n  \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n  \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n  \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n  \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n  \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n  \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n  \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/hCom2_Complex_Gut_Microbiome.html\n  \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch74/docs/communities\n  \u2713 Generated browser at /private/tmp/communitymech-causal-batch74/docs/browser.html\n  \u2713 Generated landing at /private/tmp/communitymech-causal-batch74/docs/index.html\n"
+    },
+    {
+      "check": "connectivity-survey",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-c",
+        "import json,pathlib,runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch73')),('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda:paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/connectivity-survey.log",
+      "log_sha256": "52c3470443d3c017a6c5f5ffed2fbb43348feee7fe8afbea853d97b3c39e9ed4",
+      "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 393, \"mixed\": 125, \"community_level_only\": 268, \"taxa\": 1511, \"credited_solely_by_the_rule\": 1240}, \"current\": {\"records\": 460, \"with_community_level\": 393, \"mixed\": 125, \"community_level_only\": 268, \"taxa\": 1511, \"credited_solely_by_the_rule\": 1240}}\n"
+    },
+    {
+      "check": "regressions",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "pytest",
+        "-q",
+        "tests/test_causal_review_batch10.py",
+        "tests/test_causal_review_batch11.py",
+        "tests/test_causal_review_batch12.py",
+        "tests/test_causal_review_batch13.py",
+        "tests/test_causal_review_batch14.py",
+        "tests/test_causal_review_batch15.py",
+        "tests/test_causal_review_batch16.py",
+        "tests/test_causal_review_batch17.py",
+        "tests/test_causal_review_batch18.py",
+        "tests/test_causal_review_batch19.py",
+        "tests/test_causal_review_batch20.py",
+        "tests/test_causal_review_batch21.py",
+        "tests/test_causal_review_batch22.py",
+        "tests/test_causal_review_batch23.py",
+        "tests/test_causal_review_batch24.py",
+        "tests/test_causal_review_batch25.py",
+        "tests/test_causal_review_batch27.py",
+        "tests/test_causal_review_batch28.py",
+        "tests/test_causal_review_batch29.py",
+        "tests/test_causal_review_batch30.py",
+        "tests/test_causal_review_batch31.py",
+        "tests/test_causal_review_batch32.py",
+        "tests/test_causal_review_batch33.py",
+        "tests/test_causal_review_batch34.py",
+        "tests/test_causal_review_batch35.py",
+        "tests/test_causal_review_batch36.py",
+        "tests/test_causal_review_batch37.py",
+        "tests/test_causal_review_batch38.py",
+        "tests/test_causal_review_batch39.py",
+        "tests/test_causal_review_batch40.py",
+        "tests/test_causal_review_batch41.py",
+        "tests/test_causal_review_batch42.py",
+        "tests/test_causal_review_batch43.py",
+        "tests/test_causal_review_batch44.py",
+        "tests/test_causal_review_batch45.py",
+        "tests/test_causal_review_batch46.py",
+        "tests/test_causal_review_batch47.py",
+        "tests/test_causal_review_batch48.py",
+        "tests/test_causal_review_batch49.py",
+        "tests/test_causal_review_batch5.py",
+        "tests/test_causal_review_batch50.py",
+        "tests/test_causal_review_batch51.py",
+        "tests/test_causal_review_batch52.py",
+        "tests/test_causal_review_batch53.py",
+        "tests/test_causal_review_batch54.py",
+        "tests/test_causal_review_batch55.py",
+        "tests/test_causal_review_batch56.py",
+        "tests/test_causal_review_batch57.py",
+        "tests/test_causal_review_batch58.py",
+        "tests/test_causal_review_batch59.py",
+        "tests/test_causal_review_batch6.py",
+        "tests/test_causal_review_batch60.py",
+        "tests/test_causal_review_batch61.py",
+        "tests/test_causal_review_batch62.py",
+        "tests/test_causal_review_batch63.py",
+        "tests/test_causal_review_batch64.py",
+        "tests/test_causal_review_batch65.py",
+        "tests/test_causal_review_batch66.py",
+        "tests/test_causal_review_batch67.py",
+        "tests/test_causal_review_batch68.py",
+        "tests/test_causal_review_batch69.py",
+        "tests/test_causal_review_batch7.py",
+        "tests/test_causal_review_batch70.py",
+        "tests/test_causal_review_batch71.py",
+        "tests/test_causal_review_batch72.py",
+        "tests/test_causal_review_batch73.py",
+        "tests/test_causal_review_batch74.py",
+        "tests/test_causal_review_batch8.py",
+        "tests/test_causal_review_batch9.py",
+        "tests/test_site_audit_fixes.py",
+        "tests/test_causal_review_inventory.py",
+        "tests/test_rank_causal_graph_readiness.py",
+        "tests/test_network_auditor.py",
+        "tests/test_participating_taxa.py",
+        "tests/test_causal_descriptions_are_published.py",
+        "tests/test_published_pages_name_real_records.py",
+        "tests/test_reference_validator_actually_validates.py",
+        "tests/test_snippet_audit_artefact_classes.py",
+        "tests/test_reference_error_annotation.py",
+        "tests/test_community_level_connectivity_credit.py",
+        "tests/test_no_paywalled_text_in_repo.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/regressions.log",
+      "log_sha256": "30410ca659fe377ccde3279c65585bbbc76d68d8a5fdc7cebfa009f23c4198e4",
+      "output_tail": "........................................................................ [ 10%]\n........................................................................ [ 21%]\n........................................................................ [ 32%]\n........................................................................ [ 43%]\n........................................................................ [ 54%]\n........................................................................ [ 65%]\n........................................................................ [ 76%]\n........................................................................ [ 87%]\n........................................................................ [ 97%]\n..............                                                           [100%]\n662 passed in 202.52s (0:03:22)\n"
+    },
+    {
+      "check": "black",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+        "--check",
+        "tests/test_causal_review_batch74.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/black.log",
+      "log_sha256": "1a56c7cd8457fd05d978cfbd139d7bfd86e86acaa9b57668e718ef8bccc0cf48",
+      "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n1 file would be left unchanged.\n"
+    },
+    {
+      "check": "ruff",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+        "check",
+        "tests/test_causal_review_batch74.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/ruff.log",
+      "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+      "output_tail": "All checks passed!\n"
+    },
+    {
+      "check": "diff-check",
+      "command": [
+        "git",
+        "diff",
+        "--check"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/diff-check.log",
+      "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+      "output_tail": ""
+    },
+    {
+      "check": "primary-graph-proof",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-c",
+        "import hashlib,json,pathlib,yaml\nP=pathlib.Path\nledger=yaml.safe_load(P('reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml').read_text())\nmanifest=json.loads(P('/private/tmp/communitymech-batch74/primary-manifest.json').read_text())\nsources={v['reference']:''.join(P(v['extracted_body']).read_text().split()) for v in manifest.values()}\nsources['doi:10.3390/microorganisms9020321']=sources['PMID:33557371']\nfor p,h in ledger['primary_artifacts'].items():\n assert hashlib.sha256(P(p).read_bytes()).hexdigest()==h\nfresh=visual=0\nfor row in ledger['records']:\n doc=yaml.safe_load(P(row['path']).read_text())\n for n in doc['ecological_interactions']:\n  for e in n['evidence']:\n   if e['reference'] in sources:\n    assert ''.join(e['snippet'].split()) in sources[e['reference']]\n    fresh+=1\n   else:\n    assert e['reference']=='doi:10.1016/j.ecolind.2025.114023'\n    visual+=1\nassert (fresh,visual)==(17,4)\nassert sum(len(r['node_decisions']) for r in ledger['records'])==13\nassert sum(len(r['edges_before']) for r in ledger['records'])==7\nassert sum(len(r['edges_after']) for r in ledger['records'])==3\nassert sum(len(r['removed_edge_decisions']) for r in ledger['records'])==4\nassert sum(r['curation_events_added'] for r in ledger['records'])==4\nassert ledger['edison']['provider_submissions']==0\nprint(json.dumps(dict(automatically_primary_matched=fresh,publisher_abstract_visual_matches=visual,new_nodes_or_arrows=0,complete_primary_main_texts_read=3,separate_supplements_or_original_figure_pixels_inspected=False)))\n"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/primary-graph-proof.log",
+      "log_sha256": "da6401267c02f26fef0620c5fd5c2d42c43bb39c700264c619c728181f9bca87",
+      "output_tail": "{\"automatically_primary_matched\": 17, \"publisher_abstract_visual_matches\": 4, \"new_nodes_or_arrows\": 0, \"complete_primary_main_texts_read\": 3, \"separate_supplements_or_original_figure_pixels_inspected\": false}\n"
+    },
+    {
+      "check": "focused-final",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "pytest",
+        "-q",
+        "tests/test_causal_review_batch74.py",
+        "tests/test_participating_taxa.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/focused-final.log",
+      "log_sha256": "661ce46cf0655d2a19dc9dab8b98e082fdf8f69e99aeb99b519476a9fba76b9e",
+      "output_tail": "................                                                         [100%]\n16 passed in 17.32s\n"
+    }
+  ],
+  "limitations": [
+    "Baseline before paper research covered460 records and920 caches, including both roots and ignored/hidden YAML. All13 existing nodes reviewed and retained;7 original arrows become3 after removing4 noncausal workflow/shared-outcome links. No new nodes/arrows or paid provider calls.",
+    "Full primary main bodies, embedded tables and captions read for cyanobacteria, lignocellulose and mucin. Separate supplements, raw data and original figure pixels were not audited. Moss publisher full access403; publisher-indexed primary abstract visually checked, not full Methods. Abstract-only access is not proof no controls exist.",
+    "All21 graph quotations match selected existing caches;17 also match fresh primary XML with whitespace-only normalization and4 moss quotations visually match the publisher-indexed abstract. Cache matching is not entailment. No complete primary articles added to the repository; all920 caches preserved.",
+    "Core microbiome is operational, not universal or independent of host/inoculum; plasmid content and genomic function support hypotheses, not measured exchange or fitness. Preserve positive replicated enrichment and stabilization.",
+    "Preserve formaldehyde lowering and positive growth assays; PCA control retains inhibition. Selected CM4744 methionine rescue requires added producer substrate, and C.fimi-supported methylotroph growth is a separate assay. Canonical species IDs preserved; strain metadata remains separate.",
+    "Preserve moss treatment gains and reported facilitation. Remove shared-outcome direction and reciprocal-fitness labels, not positive growth. Retain mucin substrate effects, conditional composition mediation, O/N-glycan distinction and measured profiles without inferred donor-recipient flux.",
+    "Scanned906 all-state issue titles/bodies for dedup with31 ignored/hidden local matches under explicit git/docs/site/cache exclusions. Prior957/958/959 fixes retained;1093 is unrelated cache maintenance, not a duplicate. No exhaustive historical PR-comment audit or global source-absence claim.",
+    "All raw non-graph blocks and456 other records preserved, not recertified. Metadata1624 remains OPEN after graph repair. Repair1620-1623 remain OPEN until protected-main merge. Self-adversarial COMMENT is not independent approval. The whole corpus is unfinished.",
+    "Exact HTML-description parser and repeat-render checks, not browser screenshots. Post-commit docs-current is separate."
+  ],
+  "superseded_checks": [
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-Model_Cyanobacterial_Consortia_Core_Microbiome-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch74/Model_Cyanobacterial_Consortia_Core_Microbiome-strict.tsv",
+        "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-Model_Cyanobacterial_Consortia_Core_Microbiome-strict.log",
+      "log_sha256": "d122334b9eecc0be3f02fc6a3e6c7380489f61413b9b51990adc3dbe8877ce8e",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch74/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n  files scanned:      1\n  files with ERROR:   0\n  total ERROR rows:   0\n  TSV:                /private/tmp/communitymech-batch74/Model_Cyanobacterial_Consortia_Core_Microbiome-strict.tsv\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-Model_Cyanobacterial_Consortia_Core_Microbiome-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-Model_Cyanobacterial_Consortia_Core_Microbiome-references.log",
+      "log_sha256": "baaef0ba58fee1ad13f98e141c5b119927d2adace60f760d6e4e6899182b126b",
+      "output_tail": "Validating kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n",
+      "explained_output_tail": "Validating kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-Model_Cyanobacterial_Consortia_Core_Microbiome-snippets.log",
+      "log_sha256": "6fd22c7b42f139e3b66a27210ad3d8968c80af940879c7074184305812838cca",
+      "output_tail": "# 13 evidence snippets scanned across 1 files\n  MATCH      13\n  RENDERING  0\n  ASSEMBLED  0\n  WEAK       0\n  MISMATCH   0\n  NOCONTENT  0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-Model_Cyanobacterial_Consortia_Core_Microbiome-rank.log",
+      "log_sha256": "d4967c1f7a67ba038a16c10b0a628f947cad26e9c18a183687fee0f8abc588bb",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000214\",\n    \"name\": \"Model Cyanobacterial Consortia Core Microbiome\",\n    \"score\": 65.0,\n    \"taxonomy\": 2,\n    \"connected_taxa\": 2,\n    \"disconnected_taxa\": 0,\n    \"ecological_interactions\": 3,\n    \"downstream_edges\": 0,\n    \"interaction_evidence\": 5,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"downstream\",\n      \"interaction_type\"\n    ],\n    \"path\": \"kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml\"\n  }\n]\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "Model_Cyanobacterial_Consortia_Core_Microbiome-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Model_Cyanobacterial_Consortia_Core_Microbiome/2026-10-07T024303Z-codex-050bf5.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-Model_Cyanobacterial_Consortia_Core_Microbiome-history-0.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "inventory",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "reports/causal_graph_review/build_inventory.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-inventory.log",
+      "log_sha256": "d78844fedfeacef329e7769b6dfe380bfb85d72476204febf7c2d2398c65f102",
+      "output_tail": "{\n  \"scope\": \"Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.\",\n  \"semantic_review_rule\": \"Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.\",\n  \"records\": 460,\n  \"nodes\": 1447,\n  \"edges\": 620,\n  \"records_without_nodes\": 8,\n  \"records_without_edges\": 164,\n  \"review_status_counts\": {\n    \"needs_research\": 25,\n    \"pending\": 196,\n    \"reviewed\": 239\n  },\n  \"structural_defects\": []\n}\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "network",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "communitymech.cli",
+        "audit-network",
+        "--json"
+      ],
+      "exit_code": 1,
+      "expected_exit_codes": [
+        1
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-network.log",
+      "log_sha256": "dcb33d46aa53f5e1dec55b1cd6463b83d3723e2ebf8c97999c93d0a5f4a2fed1",
+      "output_tail": "{\n          \"preferred_term\": \"Legionella MAGs\",\n          \"term\": {\n            \"id\": \"NCBITaxon:445\",\n            \"label\": \"Legionella\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The study detected Legionella-affiliated MAGs and used them in a virulence-gene risk assessment; the source did not assert pathogenicity for a cultured Legionella isolate.\\n\"\n        },\n        \"abundance_value\": \"Lower-abundance Legionella-affiliated MAGs detected during metagenomic risk assessment.\\n\",\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:41457319\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"COMPUTATIONAL\",\n            \"snippet\": \"detection of waterborne pathogens from the Legionella genus\",\n            \"explanation\": \"Supports Legionella-affiliated lower-abundance bins as monitored biosafety-relevant members of the consortium.\\n\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Legionella MAGs' has no interactions\"\n    }\n  ],\n  \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n    {\n      \"type\": \"UNKNOWN_TARGET\",\n      \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n      \"interaction_index\": 0,\n      \"taxon\": \"Sclerotinia sclerotiorum\",\n      \"severity\": \"warning\",\n      \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n    },\n    {\n      \"type\": \"UNKNOWN_TARGET\",\n      \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n      \"interaction_index\": 1,\n      \"taxon\": \"Sclerotinia sclerotiorum\",\n      \"severity\": \"warning\",\n      \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n    }\n  ],\n  \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Acinetobacter radioresistens 50V1\",\n      \"taxon_id\": \"NCBITaxon:40216\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n          \"term\": {\n            \"id\": \"NCBITaxon:40216\",\n            \"label\": \"Acinetobacter radioresistens\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"50V1\",\n          \"genome_accession\": \"GCA_002834555.1\"\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n            \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n      \"taxon_id\": \"NCBITaxon:1270\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n          \"term\": {\n            \"id\": \"NCBITaxon:1270\",\n            \"label\": \"Micrococcus luteus\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"W4-Al-K1\",\n          \"genome_accession\": \"GCA_057816565.1\"\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n            \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n      \"taxon_id\": \"NCBITaxon:64702\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n          \"term\": {\n            \"id\": \"NCBITaxon:64702\",\n            \"label\": \"Propionibacterium cyclohexanicum\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"TA-12T\",\n          \"genome_accession\": \"GCA_900111365\",\n          \"culture_collections\": [\n            {\n              \"collection\": \"DSM\",\n              \"accession\": \"16859\"\n            }\n          ]\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n            \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n      \"taxon_id\": \"NCBITaxon:219572\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n          \"term\": {\n            \"id\": \"NCBITaxon:219572\",\n            \"label\": \"Pseudomonas antarctica\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"CMS 35T\",\n          \"genome_accession\": \"GCA_010634845\",\n          \"culture_collections\": [\n            {\n              \"collection\": \"DSM\",\n              \"accession\": \"15318\"\n            }\n          ]\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n            \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n      \"taxon_id\": \"NCBITaxon:29388\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n          \"term\": {\n            \"id\": \"NCBITaxon:29388\",\n            \"label\": \"Staphylococcus capitis\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"K1-2-2-23\",\n          \"genome_accession\": \"GCA_025272695\",\n          \"culture_collections\": [\n            {\n              \"collection\": \"DSM\",\n              \"accession\": \"111179\"\n            }\n          ]\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n            \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Streptococcus halotolerans HTS9T\",\n      \"taxon_id\": \"NCBITaxon:1814128\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n          \"term\": {\n            \"id\": \"NCBITaxon:1814128\",\n            \"label\": \"Streptococcus halotolerans\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"HTS9T\",\n          \"genome_accession\": \"GCA_001598035\",\n          \"culture_collections\": [\n            {\n              \"collection\": \"DSM\",\n              \"accession\": \"101996\"\n            }\n          ]\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n            \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n    }\n  ]\n}\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "rank-all",
+      "command": [
+        "just",
+        "rank-causal-graphs"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-rank-all.log",
+      "log_sha256": "4c582286e34af3cd9d52a0aaf978ab1178bf0f007fb9731ed24962da695ec88a",
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Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n446\t100.0\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t3\t\t0\t0\n447\t100.0\tkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml\tCommunityMech:000270\tTrichoderma-Streptomyces Filamentous Cellulose Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n448\t100.0\tkb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml\tCommunityMech:000147\tTrichodesmium-Alteromonas Marine Consortium\t3\t3\t0\t3\t2\t5\t\t0\t0\n449\t100.0\tkb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "render",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "communitymech.render"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-render.log",
+      "log_sha256": "d8d9ef6f5ca625c004d6aa2bf19f5a34605d27d6ead44ce0c31bc2461a121834",
+      "output_tail": "sm.html\n  \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Bacillus_SPC.html\n  \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Ecoli_SPC.html\n  \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n  \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n  \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Saccharomyces_SPC.html\n  \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n  \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n  \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n  \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n  \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n  \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n  \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophus_Benzoate_Degrader.html\n  \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n  \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n  \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/THOR_Rhizosphere_Model_Community.html\n  \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n  \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n  \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n  \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n  \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n  \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n  \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n  \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n  \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n  \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n  \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n  \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tinto_River_Iron_Cycling_Community.html\n  \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n  \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tomato_Oxylipin_SynCom3.html\n  \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n  \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n  \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n  \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichoderma_Lactate_Platform.html\n  \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n  \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n  \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n  \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Urine_Nitrification_SynCom.html\n  \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n  \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n  \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n  \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n  \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n  \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_Consortium_C1.html\n  \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_Consortium_C6.html\n  \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n  \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n  \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n  \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n  \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n  \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n  \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n  \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n  \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n  \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n  \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n  \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n  \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/hCom2_Complex_Gut_Microbiome.html\n  \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch74/docs/communities\n  \u2713 Generated browser at /private/tmp/communitymech-causal-batch74/docs/browser.html\n  \u2713 Generated landing at /private/tmp/communitymech-causal-batch74/docs/index.html\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "render-repeat",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "communitymech.render"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-render-repeat.log",
+      "log_sha256": "d8d9ef6f5ca625c004d6aa2bf19f5a34605d27d6ead44ce0c31bc2461a121834",
+      "output_tail": "sm.html\n  \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Bacillus_SPC.html\n  \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Ecoli_SPC.html\n  \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n  \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n  \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Saccharomyces_SPC.html\n  \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n  \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n  \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n  \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n  \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n  \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n  \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophus_Benzoate_Degrader.html\n  \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n  \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n  \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/THOR_Rhizosphere_Model_Community.html\n  \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n  \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n  \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n  \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n  \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n  \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n  \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n  \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n  \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n  \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n  \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n  \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tinto_River_Iron_Cycling_Community.html\n  \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n  \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tomato_Oxylipin_SynCom3.html\n  \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n  \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n  \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n  \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichoderma_Lactate_Platform.html\n  \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n  \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n  \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n  \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Urine_Nitrification_SynCom.html\n  \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n  \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n  \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n  \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n  \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n  \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_Consortium_C1.html\n  \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_Consortium_C6.html\n  \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n  \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n  \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n  \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n  \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n  \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n  \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n  \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n  \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n  \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n  \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n  \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n  \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/hCom2_Complex_Gut_Microbiome.html\n  \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch74/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch74/docs/communities\n  \u2713 Generated browser at /private/tmp/communitymech-causal-batch74/docs/browser.html\n  \u2713 Generated landing at /private/tmp/communitymech-causal-batch74/docs/index.html\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "connectivity-survey",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-c",
+        "import json,pathlib,runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch73')),('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda:paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-connectivity-survey.log",
+      "log_sha256": "52c3470443d3c017a6c5f5ffed2fbb43348feee7fe8afbea853d97b3c39e9ed4",
+      "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 393, \"mixed\": 125, \"community_level_only\": 268, \"taxa\": 1511, \"credited_solely_by_the_rule\": 1240}, \"current\": {\"records\": 460, \"with_community_level\": 393, \"mixed\": 125, \"community_level_only\": 268, \"taxa\": 1511, \"credited_solely_by_the_rule\": 1240}}\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "regressions",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "pytest",
+        "-q",
+        "tests/test_causal_review_batch10.py",
+        "tests/test_causal_review_batch11.py",
+        "tests/test_causal_review_batch12.py",
+        "tests/test_causal_review_batch13.py",
+        "tests/test_causal_review_batch14.py",
+        "tests/test_causal_review_batch15.py",
+        "tests/test_causal_review_batch16.py",
+        "tests/test_causal_review_batch17.py",
+        "tests/test_causal_review_batch18.py",
+        "tests/test_causal_review_batch19.py",
+        "tests/test_causal_review_batch20.py",
+        "tests/test_causal_review_batch21.py",
+        "tests/test_causal_review_batch22.py",
+        "tests/test_causal_review_batch23.py",
+        "tests/test_causal_review_batch24.py",
+        "tests/test_causal_review_batch25.py",
+        "tests/test_causal_review_batch27.py",
+        "tests/test_causal_review_batch28.py",
+        "tests/test_causal_review_batch29.py",
+        "tests/test_causal_review_batch30.py",
+        "tests/test_causal_review_batch31.py",
+        "tests/test_causal_review_batch32.py",
+        "tests/test_causal_review_batch33.py",
+        "tests/test_causal_review_batch34.py",
+        "tests/test_causal_review_batch35.py",
+        "tests/test_causal_review_batch36.py",
+        "tests/test_causal_review_batch37.py",
+        "tests/test_causal_review_batch38.py",
+        "tests/test_causal_review_batch39.py",
+        "tests/test_causal_review_batch40.py",
+        "tests/test_causal_review_batch41.py",
+        "tests/test_causal_review_batch42.py",
+        "tests/test_causal_review_batch43.py",
+        "tests/test_causal_review_batch44.py",
+        "tests/test_causal_review_batch45.py",
+        "tests/test_causal_review_batch46.py",
+        "tests/test_causal_review_batch47.py",
+        "tests/test_causal_review_batch48.py",
+        "tests/test_causal_review_batch49.py",
+        "tests/test_causal_review_batch5.py",
+        "tests/test_causal_review_batch50.py",
+        "tests/test_causal_review_batch51.py",
+        "tests/test_causal_review_batch52.py",
+        "tests/test_causal_review_batch53.py",
+        "tests/test_causal_review_batch54.py",
+        "tests/test_causal_review_batch55.py",
+        "tests/test_causal_review_batch56.py",
+        "tests/test_causal_review_batch57.py",
+        "tests/test_causal_review_batch58.py",
+        "tests/test_causal_review_batch59.py",
+        "tests/test_causal_review_batch6.py",
+        "tests/test_causal_review_batch60.py",
+        "tests/test_causal_review_batch61.py",
+        "tests/test_causal_review_batch62.py",
+        "tests/test_causal_review_batch63.py",
+        "tests/test_causal_review_batch64.py",
+        "tests/test_causal_review_batch65.py",
+        "tests/test_causal_review_batch66.py",
+        "tests/test_causal_review_batch67.py",
+        "tests/test_causal_review_batch68.py",
+        "tests/test_causal_review_batch69.py",
+        "tests/test_causal_review_batch7.py",
+        "tests/test_causal_review_batch70.py",
+        "tests/test_causal_review_batch71.py",
+        "tests/test_causal_review_batch72.py",
+        "tests/test_causal_review_batch73.py",
+        "tests/test_causal_review_batch74.py",
+        "tests/test_causal_review_batch8.py",
+        "tests/test_causal_review_batch9.py",
+        "tests/test_site_audit_fixes.py",
+        "tests/test_causal_review_inventory.py",
+        "tests/test_rank_causal_graph_readiness.py",
+        "tests/test_network_auditor.py",
+        "tests/test_participating_taxa.py",
+        "tests/test_causal_descriptions_are_published.py",
+        "tests/test_published_pages_name_real_records.py",
+        "tests/test_reference_validator_actually_validates.py",
+        "tests/test_snippet_audit_artefact_classes.py",
+        "tests/test_reference_error_annotation.py",
+        "tests/test_community_level_connectivity_credit.py",
+        "tests/test_no_paywalled_text_in_repo.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-regressions.log",
+      "log_sha256": "ec1482127ec3f54b74d33d875675cee93c7389f6a6baef50b8c380d66e008a60",
+      "output_tail": "........................................................................ [ 10%]\n........................................................................ [ 21%]\n........................................................................ [ 32%]\n........................................................................ [ 43%]\n........................................................................ [ 54%]\n........................................................................ [ 65%]\n........................................................................ [ 76%]\n........................................................................ [ 87%]\n........................................................................ [ 97%]\n..............                                                           [100%]\n662 passed in 219.43s (0:03:39)\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "black",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+        "--check",
+        "tests/test_causal_review_batch74.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-black.log",
+      "log_sha256": "1a56c7cd8457fd05d978cfbd139d7bfd86e86acaa9b57668e718ef8bccc0cf48",
+      "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n1 file would be left unchanged.\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "ruff",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+        "check",
+        "tests/test_causal_review_batch74.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-ruff.log",
+      "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+      "output_tail": "All checks passed!\n",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    },
+    {
+      "check": "diff-check",
+      "command": [
+        "git",
+        "diff",
+        "--check"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch74/superseded-diff-check.log",
+      "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+      "output_tail": "",
+      "disposition": "Before stale core-evidence explanation correction; rerun required."
+    }
+  ],
+  "snippet_counts_by_record": {
+    "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml": {
+      "MATCH": 13,
+      "RENDERING": 0,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    },
+    "kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml": {
+      "MATCH": 26,
+      "RENDERING": 0,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    },
+    "kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml": {
+      "MATCH": 12,
+      "RENDERING": 0,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    },
+    "kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml": {
+      "MATCH": 28,
+      "RENDERING": 2,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    }
+  },
+  "unchanged_raw_blocks": 67,
+  "unchanged_record_files": 456,
+  "unchanged_cache_files": 920,
+  "edison": {
+    "required_for_this_repair": false,
+    "provider_submissions": 0,
+    "credits_spent": 0,
+    "rationale": "Existing topology repaired; no new causal structure. Prior denied/pending scoped authorizations unchanged."
+  },
+  "primary_artifacts": {
+    "/private/tmp/communitymech-batch74/baseline.json": "4fcf62f971101ea8197a4ac264f71e48d70b28fd2d219aa478d0f310f83d4eb9",
+    "/private/tmp/communitymech-batch74/cyanobacteria-metadata.json": "a30ed96596030facfd2665b0075e12b2f366d0c4298a061df1dfc3c15df80c50",
+    "/private/tmp/communitymech-batch74/cyanobacteria-primary.txt": "de09c8612dfc9428c7dbdd4e91689e8fd54d9e10023c22513bf57f7adc2d7f32",
+    "/private/tmp/communitymech-batch74/cyanobacteria-primary.xml": "d82ce2de2afa9ff51da61455fdd2bebd6f6422610b1a06a655e04cba47504dd9",
+    "/private/tmp/communitymech-batch74/issue-matches.json": "0e3aecfee303560a04a302b38e6ab32464a5b637846de59cea6fbed751a2f98e",
+    "/private/tmp/communitymech-batch74/lignocellulose-metadata.json": "1b81e729c0f63f16284c1bfca29582eeb1f4127a5d3353aaacdb1368cf50f35f",
+    "/private/tmp/communitymech-batch74/lignocellulose-primary.txt": "cc656b23348ad3f1f9b95b1643c541b100266b03b2725fd3c1798d07135c3124",
+    "/private/tmp/communitymech-batch74/lignocellulose-primary.xml": "9069f8368a141e4acc92553ce4ee25cc053f17b02bb71309b95a51a3c442c7ea",
+    "/private/tmp/communitymech-batch74/mucin-metadata.json": "3b0fa960f713204b88dc36d20c5aa97830fdeea369c19e4bc144d89c016de2de",
+    "/private/tmp/communitymech-batch74/mucin-primary.txt": "16874be4a038a16a34cac0b11d079c1162fb9028d3dd60afe0d59ccf65b6e39e",
+    "/private/tmp/communitymech-batch74/mucin-primary.xml": "dbbd242f1536d37ff6e6fe0a57f5ab318d4f75c433f1a66951ba6ee4d6ed43c2",
+    "/private/tmp/communitymech-batch74/primary-manifest.json": "07268fc559f6806ddea24a1c9199ba41a76ae9388e292f73cad7b3a6e834b62c"
+  },
+  "network_delta": {
+    "existing_findings_preserved": 44,
+    "added_findings": {},
+    "removed_findings": {},
+    "interpretation": "All44 baseline warnings preserved exactly. Community scope remains aggregate, not resolved member-specific activity. No taxonomy or auditor-rule changes."
+  },
+  "render_determinism": true,
+  "published_description_coverage": {
+    "pages": 456,
+    "nodes": 1433,
+    "arrows": 612
+  },
+  "participant_census": {
+    "measurements": {
+      "baseline": {
+        "records": 460,
+        "with_community_level": 393,
+        "mixed": 125,
+        "community_level_only": 268,
+        "taxa": 1511,
+        "credited_solely_by_the_rule": 1240
+      },
+      "current": {
+        "records": 460,
+        "with_community_level": 393,
+        "mixed": 125,
+        "community_level_only": 268,
+        "taxa": 1511,
+        "credited_solely_by_the_rule": 1240
+      }
+    },
+    "delta": {
+      "records": 0,
+      "with_community_level": 0,
+      "mixed": 0,
+      "community_level_only": 0,
+      "taxa": 0,
+      "credited_solely_by_the_rule": 0
+    },
+    "interpretation": "No scope-count change, taxonomy edit, or auditor-rule change. Removing group-level directional taxa does not establish member-resolved activity."
+  },
+  "network_warning_count": 44,
+  "corpus": {
+    "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+    "records": 460,
+    "nodes": 1447,
+    "edges": 620,
+    "records_without_nodes": 8,
+    "records_without_edges": 164,
+    "review_status_counts": {
+      "needs_research": 25,
+      "pending": 196,
+      "reviewed": 239
+    },
+    "structural_defects": []
+  },
+  "tested_file_sha256": {
+    "reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml": "4d975cf5114b018229e3fc8408b87ea6b43e50d5e40569c564aeefa4daffa8ca",
+    "tests/test_causal_review_batch74.py": "46f1cbe401d385001730f356bb6349965b3452c00c0f88f7b714d62f2b0c2cff",
+    "kb/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.yaml": "c995dcaed8253c17933f5cc48404f8a09438eb99dc975df2d717a08c24a69023",
+    "kb/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.yaml": "1cdf5aaf167042938bdbdd8d9bcb0abaa322a0a4a99a7f05abd8b2658740e82c",
+    "kb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml": "40f12b8a0f6ef7d64390819dd8c67282e465da6d24d5098d19080088dd04199d",
+    "kb/communities/Mucin_Glycan_MDSC_Synthetic_Gut_Community.yaml": "4ef5925538ded3549c72fd84eaa0786922b4f9565de33946289104cef18a5d49",
+    "reports/causal_graph_review/README.md": "e8279363f25533e6b67b674def497791a94daea1f4c0219c7ac961ce72542a05"
+  },
+  "status": "verified_assay_boundary_graph_review",
+  "pre_research_baseline": {
+    "base_commit": "b46d6272aa24de28b7e31995b74f7a306b387fff",
+    "base_tree": "31c6bbcfe3e24737b3f4e5291d8ed1235e53160e",
+    "research_worktree": "/private/tmp/communitymech-causal-batch73",
+    "checks": [
+      {
+        "name": "rank",
+        "command": [
+          "just",
+          "rank-causal-graphs"
+        ],
+        "exit_code": 0,
+        "expected_exit_code": 0,
+        "log": "/private/tmp/communitymech-batch74/baseline-rank.log",
+        "sha256": "d7346646f7516936c26260d0a32ae1fa38e1bd1b7afd7328411c83abfd39f2b1",
+        "output_tail": "/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+      },
+      {
+        "name": "just-network",
+        "command": [
+          "just",
+          "audit-network-json"
+        ],
+        "exit_code": 2,
+        "expected_exit_code": 2,
+        "log": "/private/tmp/communitymech-batch74/baseline-just-network.log",
+        "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+        "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n  Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+      },
+      {
+        "name": "network",
+        "command": [
+          "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+          "-m",
+          "communitymech.cli",
+          "audit-network",
+          "--json"
+        ],
+        "exit_code": 1,
+        "expected_exit_code": 1,
+        "log": "/private/tmp/communitymech-batch74/baseline-network.log",
+        "sha256": "dcb33d46aa53f5e1dec55b1cd6463b83d3723e2ebf8c97999c93d0a5f4a2fed1",
+        "output_tail": "            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \\u00b0C | 16\\u201324 h\",\n            \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Streptococcus halotolerans HTS9T\",\n      \"taxon_id\": \"NCBITaxon:1814128\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n          \"term\": {\n            \"id\": \"NCBITaxon:1814128\",\n            \"label\": \"Streptococcus halotolerans\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"HTS9T\",\n          \"genome_accession\": \"GCA_001598035\",\n          \"culture_collections\": [\n            {\n              \"collection\": \"DSM\",\n              \"accession\": \"101996\"\n            }\n          ]\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \\u00b0C | 24 h\",\n            \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n    }\n  ]\n}\n"
+      },
+      {
+        "name": "downstream",
+        "command": [
+          "rg",
+          "--no-ignore",
+          "--hidden",
+          "-n",
+          "downstream:",
+          "kb/communities",
+          "data/isolates",
+          "--glob",
+          "*.yaml"
+        ],
+        "exit_code": 0,
+        "expected_exit_code": 0,
+        "log": "/private/tmp/communitymech-batch74/baseline-downstream.log",
+        "sha256": "79f803acbc4f124d0b9bbc4715112e89d1a7e10d6f1102722b5a61b473f1f120",
+        "output_tail": "234:  downstream:\nkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml:104:  downstream:\nkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml:127:  downstream:\nkb/communities/Dual_Bacillus_coagulans_Pseudomonas_putida_Lactic_Acid_Coculture.yaml:134:  downstream:\nkb/communities/Dual_Bacillus_coagulans_Pseudomonas_putida_Lactic_Acid_Coculture.yaml:189:  downstream:\nkb/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.yaml:197:  downstream:\nkb/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.yaml:241:  downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:138:  downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:182:  downstream:\nkb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml:232:  downstream:\nkb/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.yaml:191:  downstream:\nkb/communities/Ferroplasma_Leptospirillum_Syntrophy.yaml:125:  downstream:\nkb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml:141:  downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:268:  downstream:\nkb/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.yaml:317:  downstream:\nkb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml:80:  downstream:\nkb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml:117:  downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:65:  downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:98:  downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:131:  downstream:\nkb/communities/Populus_Salt_Tolerant_SynComs.yaml:155:  downstream:\nkb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml:159:  downstream:\nkb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml:200:  downstream:\nkb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml:169:  downstream:\nkb/communities/Moss_Microbe_Complex_Regolith_Biofertilizer.yaml:199:  downstream:\n"
+      }
+    ],
+    "baseline_sha256": "4fcf62f971101ea8197a4ac264f71e48d70b28fd2d219aa478d0f310f83d4eb9"
+  },
+  "reference_validator_caveat": "All four full-record reference validators exit0. CLI Total checks counts issues, not executed checks. All21 graph quotations match selected caches;17 automatically match fresh primary XML and4 moss quotations were visually checked against the publisher-indexed primary abstract. Cache matching is not entailment. Full moss access403; all920 caches unchanged, not recertified. Prior batch73 gallium non-graph reference exception remains outside this batch."
+}
diff --git a/tests/test_causal_review_batch74.py b/tests/test_causal_review_batch74.py
new file mode 100644
index 000000000..5e950fb82
--- /dev/null
+++ b/tests/test_causal_review_batch74.py
@@ -0,0 +1,131 @@
+"""Keep positive assay results while bounding causal interpretations."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261007-four-records-batch74.yaml"
+
+
+def records():
+    ledger = yaml.safe_load(LEDGER.read_text())
+    rows = ledger["records"]
+    docs = [yaml.safe_load((ROOT / row["path"]).read_text()) for row in rows]
+    return ledger, rows, docs
+
+
+def test_core_enrichment_is_not_universal_membership_or_proven_symbiosis():
+    _, _, docs = records()
+    plasmid, function, core = docs[0]["ecological_interactions"]
+    assert plasmid["name"].startswith("Putative Plasmid")
+    assert "98%" in plasmid["description"]
+    assert "HYPOTHESIZED" in plasmid["description"]
+    assert "20 of 25" in function["description"]
+    assert "18.5%-68.5%" in core["description"]
+    assert "cyanobacteria-free controls were absent" in core["description"]
+    assert "not absence of host or inoculum effects" in core["evidence"][0]["explanation"]
+    assert "independent recruitment" not in core["evidence"][0]["explanation"]
+    assert all("interaction_type" not in node for node in [plasmid, function, core])
+    assert all("downstream" not in node for node in [plasmid, function, core])
+
+
+def test_detoxification_retains_positive_effect_and_formaldehyde_free_control():
+    _, _, docs = records()
+    toxin, mitigation, _, competition = docs[1]["ecological_interactions"]
+    assert "0.6-0.8 mM" in toxin["description"]
+    assert "0.5 mM" in toxin["description"]
+    edge = toxin["downstream"][0]
+    assert edge["target"] == mitigation["name"]
+    assert "formaldehyde-free PCA control" in edge["description"]
+    assert "lowers measurable formaldehyde" in mitigation["description"]
+    assert "not completely ameliorate" in mitigation["description"]
+    assert "secreted inhibitor" in competition["description"]
+    assert "downstream" not in competition
+
+
+def test_methionine_direction_and_conditional_rescue_are_explicit():
+    _, _, docs = records()
+    exchange = docs[1]["ecological_interactions"][2]
+    assert exchange["interaction_type"] == "CROSS_FEEDING"
+    assert exchange["source_taxon"]["term"]["id"] == "NCBITaxon:408"
+    assert exchange["target_taxon"]["term"]["id"] == "NCBITaxon:1708"
+    for term in ["CM4744", "methanol or succinate", "wild-type", "reverse-direction"]:
+        assert term in exchange["description"]
+    assert "do not demonstrate autonomous" in exchange["description"]
+    assert exchange["metabolites"][0]["term"]["id"] == "CHEBI:16811"
+
+
+def test_moss_outcomes_are_preserved_without_shared_outcome_direction():
+    ledger, _, docs = records()
+    colonization, growth, metabolites = docs[2]["ecological_interactions"]
+    assert colonization["downstream"][0]["description"].startswith("PARTIAL -")
+    assert "significant combined-treatment improvements" in growth["description"]
+    assert "downstream" not in growth
+    assert "interaction_type" not in growth and "interaction_type" not in metabolites
+    assert "D-ribose and D-gluconate" in metabolites["description"]
+    assert "parallel reported treatment outcomes" in metabolites["description"]
+    assert sum("visually matched" in s["method"] for s in ledger["snippet_checks"]) == 4
+
+
+def test_mucin_preserves_substrate_response_and_glycan_distinctions():
+    _, _, docs = records()
+    composition, degradation, fermentation = docs[3]["ecological_interactions"]
+    assert composition["downstream"][0]["description"].startswith("PARTIAL -")
+    assert "rather than holding substrate fixed" in composition["downstream"][0]["description"]
+    assert "N-glycans are completely degraded" in degradation["description"]
+    assert "some remain detectable at120 h" in degradation["description"]
+    assert "yeast-extract fermentation" in fermentation["description"]
+    assert len(docs[3]["discussions"]) == 2
+    assert (
+        docs[3]["discussions"][0]["discussion_id"] == "mucin-mdsc-pairwise-crossfeeding-resolution"
+    )
+    assert docs[3]["curation_history"][-2]["action"] == "FIX_MDSC_GTDB_GROUNDINGS"
+
+
+def test_all_nodes_and_original_arrows_have_decisions_without_extensions():
+    ledger, rows, docs = records()
+    assert sum(len(row["node_decisions"]) for row in rows) == 13
+    assert sum(len(row["edges_before"]) for row in rows) == 7
+    assert sum(len(row["edges_after"]) for row in rows) == 3
+    assert sum(len(row["removed_edge_decisions"]) for row in rows) == 4
+    assert ledger["cache_matched_graph_snippet_count"] == 21
+    assert ledger["edison"]["provider_submissions"] == 0
+    assert ledger["unresolved_non_graph_issues"] == [1624]
+    for row, doc in zip(rows, docs, strict=True):
+        renames = row["renamed_nodes"]
+        original = {
+            (renames.get(e["source"], e["source"]), renames.get(e["target"], e["target"]))
+            for e in row["edges_before"]
+        }
+        retained = {(e["source"], e["target"]) for e in row["edges_after"]}
+        removed = {
+            (renames.get(e["source"], e["source"]), renames.get(e["target"], e["target"]))
+            for e in row["removed_edge_decisions"]
+        }
+        assert original == retained | removed and not retained & removed
+        names = {n["name"] for n in doc["ecological_interactions"]}
+        assert names == {n["node"] for n in row["node_decisions"]}
+        assert all(
+            a.split("#", 1)[1] in names
+            for d in doc["discussions"]
+            for a in d["attaches_to"]
+            if a.startswith("ecological_interactions#")
+        )
+
+
+def test_record_hashes_and_append_only_histories_are_bound_to_review():
+    ledger, rows, docs = records()
+    assert ledger["independent_approval"] is False
+    for row, doc in zip(rows, docs, strict=True):
+        assert row["status"] == "reviewed" and row["outcome"] == "changed"
+        assert row["allowed_changed_fields"] == [
+            "curation_history",
+            "discussions",
+            "ecological_interactions",
+        ]
+        assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+        assert row["curation_events_added"] == len(row["history_files"]) == 1
+        assert doc["curation_history"][-1]["llm_assisted"] is True
+        assert all((ROOT / path).exists() for path in row["history_files"])