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>
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