perf(incremental): batch file-hash upserts in one transaction

persist_hashes (pipeline_incremental.c:452) upserted one file-hash row per file in autocommit -- a 10k-file reindex issued 10k separate COMMITs (each a WAL fsync). Wrap both upsert loops (current discovery + mode-skipped) in cbm_store_begin/commit so N files -> 1 COMMIT. Falls back to per-row autocommit if BEGIN fails (a caller already holds a transaction): 'batched' is gated on BEGIN's return and COMMIT runs only when BEGIN succeeded, so the existing partial-failure policy is unchanged. Fork-origin perf finding #6 (git blame: Andrew Hundt). Compiles clean (make cbm). Other perf findings are upstream-origin (cypher sort/DISTINCT, query_graph JSON, include_connected, properties re-parse -- DeusData #593/#601/#238) or fork-origin but higher-risk (deferred).

Signed-off-by: Andrew Hundt <ATHundt@gmail.com>

src/pipeline/pipeline_incremental.c

@@ -455,6 +455,12 @@ static void persist_hashes(cbm_store_t *store, const char *project, cbm_file_inf
     int current_failed = 0;
     int ms_failed = 0;
 
+    /* Batch all hash upserts in one transaction: N files -> 1 COMMIT under
+     * WAL instead of N autocommit fsyncs (a 10k-file reindex did 10k separate
+     * commits). If BEGIN fails (e.g. store busy), fall back to per-row
+     * autocommit. The partial-failure policy below is unchanged. */
+    bool batched = (cbm_store_begin(store) == CBM_STORE_OK);
+
     /* Current discovery: re-stat to capture any mtime/size that changed
      * during the run, and write fresh hash rows for visited files. */
     for (int i = 0; i < file_count; i++) {
@@ -498,6 +504,10 @@ static void persist_hashes(cbm_store_t *store, const char *project, cbm_file_inf
         }
     }
 
+    if (batched) {
+        (void)cbm_store_commit(store);
+    }
+
     if (current_failed > 0 || ms_failed > 0) {
         cbm_log_warn("incremental.persist_summary", "current_failed", itoa_buf_incr(current_failed),
                      "mode_skipped_failed", itoa_buf_incr(ms_failed));