Repair Naica inferred metabolism, ammonia-oxidation ontology and context-only arrows #1634

Scope

Naica_Deep_Subsurface_Thermophilic

High 16S GC supports inferred thermophily, not measured growth or demonstrated selection. AamoA detection supports putative oxidation, not flux. GO:0019676 is ammonia assimilation cycle, not oxidation; use GO:0019329. Remove unsupported graph concentrations and two co-occurrence/context arrows. Failed dsrA amplification is not absence, and donor limitation is proposed rather than demonstrated competition. Repair three case-inexact graph quotations without changing caches. DOI:10.3389/fmicb.2013.00037 full main body reviewed.

Deduplication

916 all-state issue titles/bodies and 27 ignored/hidden-inclusive matching local files examined; existing #1197, #1198, #939 and #396 read and preserved. No exhaustive PR-comment audit.

Acceptance

Source-bound graph repair, guarded write and append-only history; every-node/arrow decision, regression tests, actual validation outputs and self-adversarial review. Keep OPEN until protected-main merge.