fix(sync): same-named symbols keep their own cross-file callers across a re-index (#2276) (#2288)

* fix(sync): same-named symbols keep their own cross-file callers across a re-index (#2276)

Re-storing a file re-attaches the edges other files had into it by moving
each edge to the re-indexed node that replaces its target. That pairing
keyed new nodes by (kind, name) with the last one winning, so in a file
defining a name twice — the same method on two classes, a method's
overloads — any edit, even a body-only one, moved every incoming caller
of those symbols onto one of them. A body-only edit leaves the sync's
definition delta empty, so nothing re-resolved them afterwards.

The re-store now reads the file's old node identities alongside the edge
snapshot and pairs old nodes with new ones by (kind, name), then
qualified name, then signature, then position within a same-sized group
of otherwise identical nodes. A target no tier can pair one-to-one is
resurrected as its original unresolved reference, so resolution rebinds
it instead of the store guessing.

The common in-memory re-store path also now deletes the old rows, stores
the new ones and re-attaches incoming edges in one transaction. Committed
separately, a failure between the steps left the file looking new or
already current, and other files' edges into it were lost until a full
re-index.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* docs(changelog): same-named symbols keep their callers across a sync (#2276)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>

src/db/queries.ts

@@ -90,6 +90,15 @@ const IS_INTERFACE_MEMBER = (alias: string): string => `EXISTS (
  */
 export const DEPRIORITIZED_NAME_BONUS_SCALE = 0.75;
 
+/**
+ * The fields that tell one node of a file from another across a re-index of
+ * that file, whose node ids change with every line shift (#2276).
+ */
+export type NodeIdentity = Pick<
+  Node,
+  'id' | 'kind' | 'name' | 'qualifiedName' | 'signature' | 'startLine' | 'startColumn'
+>;
+
 /**
  * Database row types (snake_case from SQLite)
  */
@@ -290,6 +299,7 @@ export class QueryBuilder {
     existingNodeIdsFull?: SqliteStatement;
     getExportedNodesByFile?: SqliteStatement;
     getNodesByFileAndName?: SqliteStatement;
+    getNodeIdentitiesByFile?: SqliteStatement;
     getFileNodesByNamePrefix?: SqliteStatement;
     getNodesByQualifiedNameExact?: SqliteStatement;
     getNodesByLowerName?: SqliteStatement;
@@ -599,6 +609,15 @@ export class QueryBuilder {
     })();
   }
 
+  /**
+   * Run `fn` as one transaction. The write helpers called inside join it
+   * rather than committing on their own, so a crash part-way leaves none of
+   * `fn`'s writes behind.
+   */
+  runInTransaction<T>(fn: () => T): T {
+    return this.db.transaction(fn)();
+  }
+
   /**
    * Store one file's whole extraction bundle — nodes, edges, unresolved refs,
    * and the file record — in a SINGLE transaction. The bulk-index path calls
@@ -1033,6 +1052,31 @@ export class QueryBuilder {
     return rows.map(rowToNode);
   }
 
+  /**
+   * The {@link NodeIdentity} of every node in a file, without decoding whole
+   * nodes. Read before a re-index deletes the file, so each incoming
+   * cross-file edge can follow its target to the node that replaces it (#2276).
+   */
+  getNodeIdentitiesByFile(filePath: string): NodeIdentity[] {
+    if (!this.stmts.getNodeIdentitiesByFile) {
+      this.stmts.getNodeIdentitiesByFile = this.db.prepare(
+        'SELECT id, kind, name, qualified_name, signature, start_line, start_column FROM nodes WHERE file_path = ?'
+      );
+    }
+    const rows = this.stmts.getNodeIdentitiesByFile.all(filePath) as Array<
+      Pick<NodeRow, 'id' | 'kind' | 'name' | 'qualified_name' | 'signature' | 'start_line' | 'start_column'>
+    >;
+    return rows.map((row) => ({
+      id: row.id,
+      kind: row.kind as NodeKind,
+      name: row.name,
+      qualifiedName: row.qualified_name,
+      signature: row.signature ?? undefined,
+      startLine: row.start_line,
+      startColumn: row.start_column,
+    }));
+  }
+
   /**
    * Get all nodes in several files at once — one chunked `IN` query rather than
    * one {@link getNodesByFile} per file (#1975).
@@ -2920,13 +2964,14 @@ export class QueryBuilder {
 
   /**
    * Cross-file edges whose TARGET is a node in `filePath` and whose SOURCE is a
-   * node in a *different* file, paired with the target node's (name, kind) so a
-   * caller can re-resolve the edge to the re-indexed target's new ID (node IDs
-   * are `sha256(filePath:kind:name:line)`, so any line shift in the callee file
-   * changes target IDs and a naive re-insert by old ID silently drops them).
-   * Used by `storeExtractionResult` to preserve incoming edges across a file
-   * re-index (issue #899). Same edge-kind rules as
-   * {@link getDependentFilePaths}: all kinds except `contains`.
+   * node in a *different* file, paired with the target node's (name, kind).
+   * Node IDs are `sha256(filePath:kind:name:line)`, so any line shift in the
+   * callee file changes target IDs and a naive re-insert by old ID silently
+   * drops them; `storeExtractionResult` instead follows each old target to the
+   * re-indexed node that replaces it (see {@link getNodeIdentitiesByFile}) to
+   * preserve incoming edges across a file re-index (issue #899). Same
+   * edge-kind rules as {@link getDependentFilePaths}: all kinds except
+   * `contains`.
    */
   getCrossFileIncomingEdgesWithTarget(
     filePath: string