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Safi
d84f07c2e7
- fix SQL extractor using bare path.stem as node ID prefix — collides across same-named files in different dirs; use _file_stem() (directory-qualified) instead - fix Python import resolver keying stem_to_entities by bare stem; add bare_to_qualified secondary index for absolute imports so cross-file edges survive duplicate filenames - add stat-based mtime fastpath to file_hash: skip full SHA256 when size+mtime_ns unchanged, flush index atomically via atexit (same trade-off as make) - add cache-check, merge-chunks, merge-semantic CLI subcommands so the skill pipeline can use library functions instead of inline Python - fix absolute source_file paths from semantic subagents not being relativized before graph storage (#932): add root param to build_from_json/build/build_merge, pass scan target at both call sites - fix failed semantic chunks permanently freezing their files in the manifest (#933): filter _manifest_files to only include doc/paper/image files that appear in sem_result nodes/edges before calling save_manifest Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>