BREAKING node-ID format change. The stem that prefixes every node id was the
immediate parent dir + filename, so same-named files in different directories
collided into one last-writer-wins node and silently dropped graph content
(docs/v1/api/README.md and docs/v2/api/README.md both -> api_readme). The stem is
now the full repo-relative path (docs_v1_api_readme vs docs_v2_api_readme);
top-level files are unchanged (setup.py -> setup).
- extractors/base.py::_file_stem -> full path (as_posix; make_id collapses
separators). The two hand-copied stems (symbol_resolution, mcp_ingest) now
import the canonical one, so they can't drift again.
- llm.py system prompt + extraction-spec fragments aligned to the same rule,
fixing the #1509 AST<->LLM divergence (prompt used zero parent dirs -> ghosts).
Regenerated + blessed the per-host specs.
- build_from_json deterministically re-keys every non-AST node id from its
source_file via the new stem (and registers old-stem aliases), so a cached or
pre-migration semantic fragment carrying an old short id reconciles with the
AST node instead of spawning a ghost. The semantic cache is unversioned, so
this code-side re-key (not LLM prose) is what makes it survive the format change
with no re-bill. AST nodes are already canonical and skipped.
- Migration: existing graphs migrate automatically on the next build/update (the
re-key runs in build_from_json, including the whole graph fed back through
build_merge); `graphify extract --force` for a clean rebuild. Neo4j persisted
stores need a re-import; GraphML layouts go stale.
Full suite green (2505 passed); #1504 collision fixed and old-id fragments
re-keyed verified by smoke. Lands on v9 for review before a 0.9.0 release.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The #1033 remap relativized file node IDs but symbol IDs still embedded the
absolute parent-dir stem, so a root-level file's symbols became
<rootdir>_main_run while the file node was correctly main and the skill.md
spec (and semantic subagent) wants main_run -- splitting every top-level
file's symbols into AST/semantic ghost pairs.
Extend the remap chokepoint to also canonicalize the symbol stem prefix
(old _file_node_id(path) -> new _file_node_id(rel)), gated by source_file so
two files sharing a prefix cannot cross-contaminate. raw_calls.caller_nid is
rewritten too, since the cross-file call pass consumes it after the remap and
would otherwise dangle. No-op for nested files (immediate parent identical in
absolute and relative form).
The originally-filed root cause (facts-collector path form) was a stale-cache
red herring; the real bug is the symbol-level continuation of #1033.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
AST file nodes were ID'd from the full relative path plus extension
(match_script_pipeline_step_py) while semantic subagents follow the
{parent_dir}_{stem} spec (script_pipeline_step), so every file split
into two disconnected ghost nodes.
Fix at the single remap chokepoint in extract(): file node IDs and all
edge endpoints already funnel through the #502 relative-path remap, so
changing that remap to emit _file_node_id (one parent dir, no extension)
converts the node and every referencing edge together - Python, TS, Lua,
C and bash import edges all stay connected. symbol_resolution pre-computes
the canonical form directly (bypassing the remap) so it is synced too.
Per-site conversion (as attempted in #1038/#1065) orphans edges because
it moves the node without the edge targets; the chokepoint approach
avoids that entirely.
Backward compat for existing graphs: graphify extract --force, as the
skill.md spec already documents.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
safishamsi