Deterministic extraction, deduplication hardening, portability, and expanded test coverage

[hypnwtykvmpr]

This roll-up bundles several independent lines of work that touch extraction reliability, graph determinism, cross-machine portability, and defense against edge-case regressions.

Deterministic extraction pipeline

• A source-location pre-pass in deduplication prevents entities sharing the same (source_file, source_location) from being treated as independent, with token-level label containment to avoid wrongly merging same-line symbols.
• A prune pipeline removes stale references to nodes that no longer exist in the working tree after incremental rebuilds.
• Deterministic output: manifest.json uses sort_keys; cluster sorting is stabilized so graphify update produces repeatable output on unchanged inputs.

Portability between machines

• Manifest keys are stored root-relative instead of absolute, so graphify-out/ directories committed to git remain usable when cloned on a different machine.
• Legacy absolute keys in manifests are normalized at load time, including macOS /var to /private/var symlink resolution.

Edge-case hardening

Eight defects found through systematic review of the build, dedup, detect, extract, watch, and symbol_resolution modules were resolved:

• Stale nodes from deleted or modified source files no longer survive incremental graph merges.
• Watch rebuilds now filter preserved nodes whose source files have been removed.
• build_from_json guards against collapsing parallel edges with different relation types between the same endpoints.
• Intra-file call resolution detects ambiguous duplicate labels and prefers scope-qualified labels over bare ones.
• Cross-file call resolvers now track (source, target, relation) triples instead of only (source, target) pairs.
• Source-location dedup uses token-level rather than character-level substring containment.
• Incremental detection no longer skips content re-hashing when a file's mtime hasn't changed within the second-resolution filesystem clock.
• Normalized endpoint ID collision detection with overlap threshold and suffix disambiguation.

Additional file format support

• .json and .jsonc are now indexed as document types alongside .yaml and .yml for document extraction.

Test coverage

• Added unit tests spanning cache, dedup, export, ingest, llm_backends, security, tree_html, cluster, detect, manifest, and watch modules.
• pytest.importorskip guards added for optional dependency imports to keep the suite green on GitHub CI.

69 files changed, +21,176 / -725 lines

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[safishamsi]

Thanks for the large rollup — there are real improvements here (manifest portability, dedup pre-pass, Leiden seed, community sort stability). However the PR as submitted has a few blockers and is too large to merge safely as a single unit.

Blockers

1. Breaking API change in deduplicate_entities()

The return type changed from (nodes, edges) to (nodes, edges, hyperedges, stats) without being flagged. Any external caller (downstream scripts, integrations, forks) will break silently. This needs to be documented as a breaking change, and all call sites in the repo verified.

2. Edge collapse fix is incomplete

The "first relation wins" logic in build_from_json uses ordered (src, tgt) pairs. For an undirected nx.Graph, a B→A edge arriving after A→B with a different relation will be silently overwritten by NetworkX — the new collision counter won't catch it. The fix doesn't achieve determinism without guaranteed upstream edge ordering.

3. Fork is inaccessible (404)

The source repo is currently returning 404, which prevents full-file context verification for the review. Please ensure the branch is publicly accessible.

4. No CI

No checks ran on this PR. All other merged PRs in this repo have CI green before merge.

Recommended: split into focused PRs

At 21,176 lines in a single commit this exceeds review tooling limits. Each of these is independently mergeable and reviewable:

• Portability: detect.py / cache.py / watch.py relative-path machinery
• Dedup pre-pass: _source_location_dedup + prune_graph_references in dedup.py
• Build determinism: build_from_json edge collapse + sort_keys
• New modules: symbol_resolution.py, scip_ingest.py, semantic_facts.py, deterministic_docs.py — each deserves its own PR with rationale

Happy to merge each piece once it comes in separately with CI green.