fix: add migration v20 for conflict retry columns + serialize worktree ops

db.py: migration v20 adds conflict_rebase_attempts, merge_failures,
merge_cycled columns (already exist on VPS via manual migration, missing
from code — any future DB rebuild would break retry mechanism).

merge.py: replace retry-with-backoff on config.lock with asyncio.Lock
(_bare_repo_lock) around all worktree add/remove calls. Prevents
contention instead of retrying it. Applied to both _cherry_pick_onto_main
and _merge_reweave_pr.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

lib/db.py

@@ -9,7 +9,7 @@ from . import config
 
 logger = logging.getLogger("pipeline.db")
 
-SCHEMA_VERSION = 19
+SCHEMA_VERSION = 20
 
 SCHEMA_SQL = """
 CREATE TABLE IF NOT EXISTS schema_version (
@@ -533,6 +533,19 @@ def migrate(conn: sqlite3.Connection):
         conn.commit()
         logger.info("Migration v19: added submitted_by to prs and sources tables")
 
+    if current < 20:
+        for col, default in [
+            ("conflict_rebase_attempts", "INTEGER DEFAULT 0"),
+            ("merge_failures", "INTEGER DEFAULT 0"),
+            ("merge_cycled", "INTEGER DEFAULT 0"),
+        ]:
+            try:
+                conn.execute(f"ALTER TABLE prs ADD COLUMN {col} {default}")
+            except sqlite3.OperationalError:
+                pass
+        conn.commit()
+        logger.info("Migration v20: added conflict retry columns to prs")
+
     if current < SCHEMA_VERSION:
         conn.execute(
             "INSERT OR REPLACE INTO schema_version (version) VALUES (?)",

lib/merge.py

@@ -57,6 +57,9 @@ logger = logging.getLogger("pipeline.merge")
 # In-memory domain locks — fast path, lost on crash (durable layer is prs.status)
 _domain_locks: dict[str, asyncio.Lock] = defaultdict(asyncio.Lock)
 
+# Bare repo lock — serializes worktree add/remove to prevent config.lock contention
+_bare_repo_lock = asyncio.Lock()
+
 # Merge timeout: if a PR stays 'merging' longer than this, force-reset (Rhea)
 MERGE_TIMEOUT_SECONDS = 300  # 5 minutes
 
@@ -314,14 +317,8 @@ async def _cherry_pick_onto_main(branch: str) -> tuple[bool, str]:
 
     commit_list = [c.strip() for c in commits_out.strip().split("\n") if c.strip()]
 
-    # Create worktree from origin/main (fresh branch)
+    # Serialize worktree add/remove — concurrent calls hit bare repo config.lock
-    # Delete stale local branch if it exists from a previous failed attempt
+    async with _bare_repo_lock:
-    await _git("branch", "-D", clean_branch)
-    rc, out = await _git("worktree", "add", "-b", clean_branch, worktree_path, "origin/main")
-    for _retry in range(3):
-        if rc == 0 or "could not lock config" not in out:
-            break
-        await asyncio.sleep(random.uniform(0.5, 2.0 * (_retry + 1)))
         await _git("branch", "-D", clean_branch)
         rc, out = await _git("worktree", "add", "-b", clean_branch, worktree_path, "origin/main")
     if rc != 0:
@@ -407,9 +404,9 @@ async def _cherry_pick_onto_main(branch: str) -> tuple[bool, str]:
         return True, "cherry-picked and pushed"
 
     finally:
-        # Cleanup worktree and temp branch
+        async with _bare_repo_lock:
-        await _git("worktree", "remove", "--force", worktree_path)
+            await _git("worktree", "remove", "--force", worktree_path)
-        await _git("branch", "-D", clean_branch)
+            await _git("branch", "-D", clean_branch)
 
 
 REWEAVE_EDGE_FIELDS = ("supports", "challenges", "challenged_by", "depends_on", "related", "reweave_edges")
@@ -575,14 +572,8 @@ async def _merge_reweave_pr(branch: str) -> tuple[bool, str]:
     if not changed_files:
         return False, "no .md files changed"
 
-    # Pre-cleanup: remove stale worktree/branch from prior crash (SIGKILL, OOM, etc.)
+    async with _bare_repo_lock:
-    await _git("worktree", "remove", "--force", worktree_path)
+        await _git("worktree", "remove", "--force", worktree_path)
-    await _git("branch", "-D", clean_branch)
-    rc, out = await _git("worktree", "add", "-b", clean_branch, worktree_path, "origin/main")
-    for _retry in range(3):
-        if rc == 0 or "could not lock config" not in out:
-            break
-        await asyncio.sleep(random.uniform(0.5, 2.0 * (_retry + 1)))
         await _git("branch", "-D", clean_branch)
         rc, out = await _git("worktree", "add", "-b", clean_branch, worktree_path, "origin/main")
     if rc != 0:
@@ -689,8 +680,9 @@ async def _merge_reweave_pr(branch: str) -> tuple[bool, str]:
         return True, result_msg
 
     finally:
-        await _git("worktree", "remove", "--force", worktree_path)
+        async with _bare_repo_lock:
-        await _git("branch", "-D", clean_branch)
+            await _git("worktree", "remove", "--force", worktree_path)
+            await _git("branch", "-D", clean_branch)
 
 
 async def _resubmit_approvals(pr_number: int):