fix(resolution): sweep orphaned unresolved refs so an interrupted index heals on sync (#1187) (#1191)

An indexing run killed mid-"Resolving refs" (crash, Ctrl-C, the #1122
watchdog kill) left the refs it never reached parked in unresolved_refs.
The git-scoped sync fast path only re-resolves changed files' refs, so
those files' call edges were missing permanently — a too-small blast
radius clustering by package/module (the #1187 field report: 3 of 10
caller files for a Spring @Resource-injected method) — until a full
re-index.

- sync() now sweeps leftover unresolved refs with the batched resolver
  after its scoped pass, including on no-change syncs, so a bare
  `codegraph sync` recovers a wedged index (and heals pre-fix indexes
  on the first post-upgrade sync)
- the scoped pass deletes unresolvable rows too (parity with the
  batched path), making "rows at rest" a sound orphan signal
- drop the batched loop's early break that abandoned all later batches
  when one batch was all-unresolvable (its rows WERE consumed — that
  early stop could orphan the rest of the table at init)
- surface the state: `codegraph status` warns, `status --json` gains
  index.pendingRefs, and MCP codegraph_status tells agents the blast
  radius is incomplete until the next sync

Verified end-to-end on a 2,414-file synthetic Spring repo: SIGKILL
mid-resolution reproduces the reporter's exact 3-of-10-callers state;
a bare sync now heals it to 10/10 with the edge count converging to
the clean-init total; a healthy-index sync stays a no-op.

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

src/mcp/tools.ts

@@ -4038,6 +4038,19 @@ export class ToolHandler {
       );
     }
 
+    // Non-zero at rest means a resolution pass was interrupted mid-run, so
+    // some files' call/impact edges are missing until the next sync sweeps
+    // the leftovers (#1187). Surface it — an agent trusting an incomplete
+    // blast radius is worse than one that knows to re-sync.
+    const pendingRefs = cg.getPendingReferenceCount();
+    if (pendingRefs > 0) {
+      lines.push(
+        `**Pending resolution:** ⚠ ${pendingRefs} references from an interrupted ` +
+        `index run — some caller/impact edges are missing until the next sync ` +
+        `(any file change triggers it, or run \`codegraph sync\`)`
+      );
+    }
+
     lines.push('', '**Nodes by Kind:**');
 
     for (const [kind, count] of Object.entries(stats.nodesByKind)) {