4c15f84aa4
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>