* feat(cli): expose caller-selected reference-source path exclusions
Let import-reference-source accept a JSON array of Git-ignore rules and
pass them to the existing importer before the source tree is opened.
Fixes#2443
* docs(cli): use an effective reference exclusion negation
* test(cli): expect entry_kind on reference-source exclusions
Main records entry_kind on every historical source exclusion. The caller
exclusion assertions still compared objects without that field, so the
pruning test failed after merging main.
Co-authored-by: Yunzhou Li <YunzhouLi-hub@users.noreply.github.com>
* test(cli): record caller *.tmp over project ignore
Caller exclusions are mandatory and override project rules, so project.tmp
matched by *.tmp is caller-excluded. Align the pruning assertion with that
result from the merged importer.
---------
Co-authored-by: morluto <76467478+morluto@users.noreply.github.com>
Co-authored-by: REA Maintenance <rea-maintenance@users.noreply.github.com>
Co-authored-by: Cursor Agent <cursoragent@cursor.com>
Co-authored-by: Yunzhou Li <YunzhouLi-hub@users.noreply.github.com>
Normalize path facts once at the owning filesystem boundary, preserve caller spelling and unavailable inventory members, and retain typed read failures. Record exclusion entry kinds so only proven directories can establish descendant symlink targets; omitted legacy kinds stay unknown.
Reviewed fixes include #1969, #2642, #2759, and #2994.
Validation: 26 reference graph source tests passed; prior artifact checks passed 275 tests with one Windows-only skip. Updated compiled import workflows are included in final validation after regeneration.
Record the exact matching pattern and distinguish project, default, caller, and configured-sensitive exclusions without changing ignore ordering. Include that provenance in graph commitments and validate the contract through compiled CLI and MCP consumers.
BREAKING CHANGE: Pattern-based reference graph exclusions require pattern and distinguish project-ignored and default-ignored reasons. Re-import saved graphs that omit matching patterns.
