feat: corpus knowledge graph module (organvm corpus)

[4444J99]

Summary

Build organvm_engine/corpus/ module — a computational bridge between the post-flood constitutional corpus (225 files) and praxis-perpetua operational corpus (2,728 files).

IRF Reference

IRF-SYS-104 — Corpus Knowledge Graph

Background

Cross-reference analysis (S-corpus-graph, 2026-04-07/08) revealed:

• Strong connections: AMMOI, Alpha-Omega, Formation Protocol, SPEC notation
• Gaps: SVSE under-referenced, Faculty/Commission/Defense governance minimally cross-linked
• No computational cross-corpus index exists — concepts are the connective tissue but have no graph representation

Scope

• 4-phase extraction pipeline (structural scan → concept enumeration → implementation links → SPEC cross-refs)
• data/concept-seed.yaml bootstrap (~30 canonical concepts with aliases)
• JSON graph store (~500 nodes, ~3,000 edges, <1MB)
• 6 navigable markdown indices: concept-index, provenance-map, spec-coverage, tag-analysis, cross-corpus-bridges, gaps
• Extend RelationType (+5: DEFINES, REFERENCES, IMPLEMENTS, GROUNDS, EXTRACTED_FROM)
• Extend EntityType (+3: CONCEPT, SPEC, TRANSCRIPT)
• CLI: organvm corpus build|render|query|gaps|stats

Plan

post-flood/.claude/plans/2026-04-07-corpus-knowledge-graph.md

Integration Points

• organvm-engine/src/organvm_engine/ontology/relations.py — RelationType enum + Relation dataclass
• organvm-ontologia/src/ontologia/entity/identity.py — EntityType enum
• organvm-engine/src/organvm_engine/indexer/scanner.py — walk_repo() pattern

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Backlog engagement 2026-07-19 — disposition: distilled.

Verified delivered on current main: the corpus graph module exists at src/organvm_engine/corpus/graph.py and scanner.py, CLI commands live in src/organvm_engine/cli/corpus.py, and tests/test_corpus.py covers graph nodes/edges, sidecar/frontmatter/seed scanning, gaps, trace, coverage, and repo concepts. Open PR #140 is now stale/red relative to this mainline implementation.