fix(build_merge): replace re-extracted files instead of accumulating stale edges#1344
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safishamsi merged 1 commit intoJun 17, 2026
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…stale edges build_merge merged the loaded graph (base) with new_chunks and only collapsed exact-duplicate edges via dedupe_edges. When a file CHANGED, build() merged its old and new contributions for the same source_file, so any node/edge that disappeared from the file's new version survived forever — stale edges accumulated across every incremental `extract` update. Only fully DELETED files were cleaned (via prune_sources); changed files were never pruned. Fix: before merging, drop from the loaded base every node/edge whose source_file is present in new_chunks, so a re-extracted file REPLACES its prior contribution. Brand-new files aren't in base (no-op); deleted files are still handled by prune_sources. Matched in both raw and _norm_source_file form so an absolute win32 path in new_chunks still matches the relative posix source_file stored in the graph (mirrors the prune path, Graphify-Labs#1007). Adds a regression test covering: stale node/edge dropped, fresh node/edge present, unchanged file untouched, and win32 absolute new-chunk path matching.
This was referenced Jun 17, 2026
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safishamsi
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Jun 18, 2026
…eleted-only Completes the source_file convention fix begun in #1344 (build_merge replace-on-re-extract) and #1361 (pass root= to build_merge in the --update runbook). Two gaps still let the full build and incremental --update emit different source_file bases for the same file, so the source_file-keyed replace missed and duplicates accumulated: 1. extraction-spec(.md/-compact.md): the subagent's source_file slot was an unpinned "relative/path", so it invented a base per run (and the node id, derived from the same path, drifted too). Pin it to the verbatim FILE_LIST path so _norm_source_file(root) canonicalizes every run identically. 2. core.md: the full build called build_from_json WITHOUT root=, so #1361's update-side root= had no matching base on the full-build side. Pass root='INPUT_PATH' at both sites (Step 4 export, Step 5 report) so the full build and --update relativize to the same base. update.md prune_sources = deleted only. Changed files are replaced by build_merge (#1344); once root= aligns the bases, leaving `changed` in prune_sources would delete the freshly re-extracted nodes. Engine (build.py) unchanged. Regenerated all skill artifacts via tools/skillgen/gen.py. Adds test_build_merge_root_collapses_convention_drift. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
safishamsi
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Jun 18, 2026
…tops duplicating After #1361 added root= to the --update build_merge call, build_merge's prune (which runs after the merge) began matching freshly re-extracted changed-file nodes and deleting them — a regression in 0.8.41 where --update on a changed file wiped its nodes. This drops `changed` from prune_sources (replace-on- re-extract from #1344 already reconciles changed files), passes root= to the full build's build_from_json so its node-key base matches the update side, and pins the extraction-spec source_file to the verbatim path so the two runs never drift. Re-blessed skillgen expected/ snapshots. Co-Authored-By: RelywOo <RelywOo@users.noreply.github.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
galshubeli
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Jun 18, 2026
Resolve conflicts after upstream advanced (Java records, Swift relationships, build_merge replace-on-re-extract Graphify-Labs#1344, dedup fixes, HTML XSS hardening, etc.): - build.py build_merge: adopt v8's replace-on-re-extract (Graphify-Labs#1344/Graphify-Labs#1007) — drop a changed file's prior source_file contribution before merging so stale nodes/edges don't accumulate — but keep loading the base from the FalkorDB store (not graph.json), and keep graph_name/uri binding. - skillgen update fragment: keep the FalkorDB _store/open_store binding for the --update build_merge call; fold in v8's root= prune-relativization note (Graphify-Labs#1361). Regenerated skill artifacts + blessed goldens. - test_build.py: keep the store-based tests; v8's new graph.json/build_merge(path) tests don't apply to the store-based build_merge. Verified: package imports, zero runtime networkx, 118 merge-relevant tests pass (1 env-only tree-sitter fail), skillgen --check clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
antonioscarinci
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Jun 27, 2026
Combines v8's features (uv/pipx detection, graphify-out/ convention, FalkorDB, Step 4.5 health check, directed-graph support, shrink-guard, build_merge --update) with windows-skill-fix's approach (PowerShell throughout, external windows-scripts/*.py, fail-fast, incremental --update fix, Windows encoding fixes). Key changes: - windows-scripts/: all 34 scripts ported to graphify-out/ paths and v8 API (root=, cache_root=, directed=, build_from_json, etc.) - detect_incremental.py: propagates all_files so manifest covers full corpus on --update, not just changed files - check_graph_health.py: new script wrapping v8's diagnostics step - skill-windows.md: rewritten for PowerShell with $GRAPHIFY_SCRIPTS loaded from file each step; --update uses inline build_merge() so edge direction is preserved (Graphify-Labs#801, Graphify-Labs#1344, Graphify-Labs#1361) - export.py: replace None attribute values before nx.write_graphml to avoid AttributeError on None-valued node/edge properties - __main__.py: add --answer-file to graphify save-result to bypass Windows command-line length limit for long answers - .gitattributes: add line-ending normalization rules for .py/.sh (LF) and .bat/.cmd (CRLF) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Problem
build_mergemerges the loaded graph (base) withnew_chunksand only collapses exact-duplicate edges viadedupe_edges. When a file changed,build()merged its old and new contributions for the samesource_file, so any node/edge that disappeared from the file's new version survived forever — stale edges accumulate across every incrementalextractupdate. Only fully deleted files were cleaned (viaprune_sources); changed files were never pruned.Repro: build a graph where
changed.mdyieldsA,B+ edgeA->B, thenbuild_mergewith a re-extraction ofchanged.mdyieldingA,C+ edgeA->C. The oldA->Bedge and orphanBsurvive alongside the freshA->C.Fix
Before merging, drop from the loaded base every node/edge whose
source_fileis present innew_chunks, so a re-extracted file replaces its prior contribution.prune_sources._norm_source_fileform, so an absolute win32 path innew_chunksstill matches the relative posixsource_filestored in the graph (mirrors the prune path, Bug: Nodes and edges from deleted/moved files persist in graph — "already clean" false negative #1007).Docstring updated:
build_mergenow documents replace-on-re-extract semantics instead of "only grows".Test
Adds
test_build_merge_replaces_changed_file_stale_edges:Full
tests/test_build.pygreen (33 passed).