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>

src/gitlab/transformers/merge_request.rs

@@ -24,6 +24,8 @@ pub struct NormalizedMergeRequest {
     pub closed_at: Option<i64>,
     pub last_seen_at: i64,
     pub web_url: String,
+    pub merge_commit_sha: Option<String>,
+    pub squash_commit_sha: Option<String>,
 }
 
 #[derive(Debug, Clone)]
@@ -100,6 +102,8 @@ pub fn transform_merge_request(
             closed_at,
             last_seen_at: now_ms(),
             web_url: gitlab_mr.web_url.clone(),
+            merge_commit_sha: gitlab_mr.merge_commit_sha.clone(),
+            squash_commit_sha: gitlab_mr.squash_commit_sha.clone(),
         },
         label_names: gitlab_mr.labels.clone(),
         assignee_usernames,

src/gitlab/types.rs

@@ -247,4 +247,6 @@ pub struct GitLabMergeRequest {
     #[serde(default)]
     pub reviewers: Vec<GitLabReviewer>,
     pub web_url: String,
+    pub merge_commit_sha: Option<String>,
+    pub squash_commit_sha: Option<String>,
 }

src/ingestion/merge_requests.rs

@@ -180,8 +180,9 @@ fn process_mr_in_transaction(
             author_username, source_branch, target_branch, head_sha,
             references_short, references_full, detailed_merge_status,
             merge_user_username, created_at, updated_at, merged_at, closed_at,
-            last_seen_at, web_url, raw_payload_id
-        ) VALUES (?1, ?2, ?3, ?4, ?5, ?6, ?7, ?8, ?9, ?10, ?11, ?12, ?13, ?14, ?15, ?16, ?17, ?18, ?19, ?20, ?21, ?22)
+            last_seen_at, web_url, raw_payload_id,
+            merge_commit_sha, squash_commit_sha
+        ) VALUES (?1, ?2, ?3, ?4, ?5, ?6, ?7, ?8, ?9, ?10, ?11, ?12, ?13, ?14, ?15, ?16, ?17, ?18, ?19, ?20, ?21, ?22, ?23, ?24)
         ON CONFLICT(gitlab_id) DO UPDATE SET
             title = excluded.title,
             description = excluded.description,
@@ -200,7 +201,9 @@ fn process_mr_in_transaction(
             closed_at = excluded.closed_at,
             last_seen_at = excluded.last_seen_at,
             web_url = excluded.web_url,
-            raw_payload_id = excluded.raw_payload_id",
+            raw_payload_id = excluded.raw_payload_id,
+            merge_commit_sha = excluded.merge_commit_sha,
+            squash_commit_sha = excluded.squash_commit_sha",
         params![
             mr_row.gitlab_id,
             project_id,
@@ -224,6 +227,8 @@ fn process_mr_in_transaction(
             now,
             &mr_row.web_url,
             payload_id,
+            &mr_row.merge_commit_sha,
+            &mr_row.squash_commit_sha,
         ],
     )?;
 
@@ -368,7 +373,8 @@ fn reset_discussion_watermarks(conn: &Connection, project_id: i64) -> Result<()>
          SET discussions_synced_for_updated_at = NULL,
              discussions_sync_attempts = 0,
              discussions_sync_last_error = NULL,
-             resource_events_synced_for_updated_at = NULL
+             resource_events_synced_for_updated_at = NULL,
+             closes_issues_synced_for_updated_at = NULL
          WHERE project_id = ?",
         [project_id],
     )?;

src/ingestion/orchestrator.rs

@@ -785,9 +785,32 @@ fn update_resource_event_watermark(
     Ok(())
 }
 
+fn update_closes_issues_watermark(conn: &Connection, mr_local_id: i64) -> Result<()> {
+    conn.execute(
+        "UPDATE merge_requests SET closes_issues_synced_for_updated_at = updated_at WHERE id = ?",
+        [mr_local_id],
+    )?;
+    Ok(())
+}
+
 fn enqueue_mr_closes_issues_jobs(conn: &Connection, project_id: i64) -> Result<usize> {
-    let mut stmt =
-        conn.prepare_cached("SELECT id, iid FROM merge_requests WHERE project_id = ?1")?;
+    // Remove stale jobs for MRs that haven't changed since their last closes_issues sync
+    conn.execute(
+        "DELETE FROM pending_dependent_fetches \
+         WHERE project_id = ?1 AND entity_type = 'merge_request' AND job_type = 'mr_closes_issues' \
+           AND entity_local_id IN ( \
+               SELECT id FROM merge_requests \
+               WHERE project_id = ?1 \
+                 AND updated_at <= COALESCE(closes_issues_synced_for_updated_at, 0) \
+           )",
+        [project_id],
+    )?;
+
+    let mut stmt = conn.prepare_cached(
+        "SELECT id, iid FROM merge_requests \
+         WHERE project_id = ?1 \
+           AND updated_at > COALESCE(closes_issues_synced_for_updated_at, 0)",
+    )?;
     let entities: Vec<(i64, i64)> = stmt
         .query_map([project_id], |row| Ok((row.get(0)?, row.get(1)?)))?
         .collect::<std::result::Result<Vec<_>, _>>()?;
@@ -886,6 +909,7 @@ async fn drain_mr_closes_issues(
                     match store_result {
                         Ok(()) => {
                             complete_job(conn, job.id)?;
+                            update_closes_issues_watermark(conn, job.entity_local_id)?;
                             result.fetched += 1;
                         }
                         Err(e) => {
@@ -907,6 +931,7 @@ async fn drain_mr_closes_issues(
                             "Permanent API error for closes_issues, marking complete"
                         );
                         complete_job(conn, job.id)?;
+                        update_closes_issues_watermark(conn, job.entity_local_id)?;
                         result.skipped_not_found += 1;
                     } else {
                         warn!(