Repair workflow and causal-direction claims in denitrifying diversity graph #1704

CommunityMech:000113; PMID37207729. Remove two engineering/evolution-workflow nodes already represented in engineering_design and their arrows. Preserve experimental DR function/stability, Paracoccus-dominated denitrification, and overyielding/asynchrony/complementarity results. Remove two endpoint-to-component/decomposition arrows; these do not establish the stated causal directions. Dominance is not demonstrated resource competition and aggregate complementarity is not compound-resolved niche partitioning. No new reversed edge without Edison workflow. Close only after protected-main merge.

Dedup: 978 all-state issue titles/bodies; matched closed #1116/#1117/#1118 read. Exact IDs, PMIDs, DOIs, record names and CCMA strains included. Local hidden/ignored-inclusive search found 43 files, excluding .git/docs/site/references_cache. Four primary cache files separately read. Comments/PRs not exhaustively searched. Fresh baseline preceded sources. Source-based self-adversarial review, not independent approval.