feat(biomarkers): graph-aware god_class + feature_envy rules#133

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andreinknv wants to merge 70 commits into

colbymchenry:mainfrom

andreinknv:feat/biomarkers-graph-rules

Commits on Apr 26, 2026

feat: index files inside git submodules

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docs: README setup snippets for non-Claude MCP clients

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docs: cookbook for adding a new language

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fix: correctness bugs found in audit

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fix: defense-in-depth hardening

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fix(sync): detect HEAD-moving git operations to prevent stale index

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fix: extraction/resolution accuracy (BOM, comment-strip retry, framework regex)

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fix: also strip comments before C# minimal-API route regex

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fix(db): enforce UNIQUE on edges so INSERT OR IGNORE actually dedupes

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fix(scan): honor .codegraphignore on the git fast path

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feat(search): subword tokens + Porter stemmer + stopword filter for FTS

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feat(cochange): file-level co-change graph mined from git history

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feat(graph): convention-based tests-as-edges (test file → subject file)

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feat(search): per-file diversification so top-K isn't one class's methods

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perf(db): batch node lookups, fix insertNode cache, auto-ANALYZE after writes

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test(watcher): fix fs.watch flake by adding settle delay before file write

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feat(mcp): codegraph_review_context — structured PR-review context from a diff

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feat: LLM symbol summaries with auto-detect + background execution

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feat: semantic search, hybrid retrieval, Q&A, cross-language matching

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feat: tier 1-3 LLM features + agent-as-LLM bridge

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fix: directory summary column-order swap (summary <-> content_hash)

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Commits on Apr 27, 2026

Commits on Apr 28, 2026