feat: Add commit SHAs, closes_issues watermark, and PRD alignment

Migration 015 adds merge_commit_sha/squash_commit_sha to merge_requests
(Gate 4/5 prerequisites), closes_issues_synced_for_updated_at watermark
for incremental sync, and the missing idx_label_events_label index.

The MR transformer and ingestion pipeline now populate commit SHAs during
sync. The orchestrator uses watermark-based filtering for closes_issues
jobs instead of re-enqueuing all MRs every sync.

The Phase B PRD is updated to match the actual codebase: corrected
migration numbering (011-015), documented nullable label/milestone
fields (migration 012), watermark patterns (013), observability
infrastructure (014), simplified source_method values, and updated
entity_references schema to match implementation.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

tests/mr_transformer_tests.rs

@@ -51,6 +51,8 @@ fn make_test_mr() -> GitLabMergeRequest {
             name: "Alice Wong".to_string(),
         }],
         web_url: "https://gitlab.example.com/group/project/-/merge_requests/42".to_string(),
+        merge_commit_sha: Some("merge1234567890".to_string()),
+        squash_commit_sha: None,
     }
 }
 
@@ -98,6 +100,18 @@ fn transforms_mr_with_all_fields() {
     );
 }
 
+#[test]
+fn preserves_commit_shas() {
+    let mr = make_test_mr();
+    let result = transform_merge_request(&mr, 200).unwrap();
+
+    assert_eq!(
+        result.merge_request.merge_commit_sha,
+        Some("merge1234567890".to_string())
+    );
+    assert!(result.merge_request.squash_commit_sha.is_none());
+}
+
 #[test]
 fn parses_timestamps_to_ms_epoch() {
     let mr = make_test_mr();