`storeExtractionResult` deletes a re-indexed file's nodes via `deleteFile`,
which cascades through `edges.FK ... ON DELETE CASCADE` to delete every edge
whose source OR target is one of those nodes. Edges whose source is in the
re-indexed file are re-emitted by the extractor, but edges whose source is in
a *different* (unchanged) file are not — they are silently dropped. This is
issue #899: re-indexing a callee file severs `calls`/`references` edges from
callers that import it via module-attribute access (`pkg.mod.fn(...)`), so
`codegraph callers fn` reports 0 callers for functions that have real call
sites. A docstring-only edit on the callee is sufficient to trigger it.
The bug affects every incremental path that routes through `sync()` /
`indexFile()`: `codegraph sync`, the file-watcher auto-sync (which calls
`sync()`), and the git sync hooks. `codegraph index` was already fixed by
#894 (it now clears-then-rebuilds, so it's a full re-extraction, not
incremental). `sync` remains the fast incremental path and still has the bug.
Fix: before the delete, snapshot incoming cross-file edges paired with the
target node's (name, kind). After re-inserting the file's nodes + same-file
edges, re-insert the snapshot — re-resolving each edge's target to the
re-indexed node's NEW id by (filePath, kind, name). Node ids are
`sha256(filePath:kind:name:line)`, so any line shift in the callee file (e.g.
a docstring-only edit above the symbol) changes every target id and a naive
re-insert by old id would drop them all. Matching by (kind, name) is stable
across line shifts; if the symbol was renamed/removed, no match is found and
the edge stays dropped (correct). `insertEdges` still filters to endpoints
that exist, so edges whose caller (source) was deleted are also dropped.
Regression tests in `__tests__/sync.test.ts` model the RAGFlow production
case: a `pkg/mod.py` with two callees, both called from `test/test_callers.py`
via `mod.<fn>(...)`. The first test confirms a docstring-only edit that shifts
the second callee's line preserves both incoming edges. The second test
confirms renaming a callee correctly drops its old incoming edge (no phantom
preservation against a non-existent symbol).
