fix(worktree-audit): make cleanup audit merged-PR aware for issue worktrees (Closes #858)

gitea_audit_worktree_cleanup had no PR linkage. Issue worktrees therefore
reported pr_number=null and classified as active_issue_work with
removable=false permanently, even once their PR was merged and the head was
already contained in master. Observed on live master 9301739910: 42
issue_work worktrees, 0 removable, 0 with pr_number populated, while
gitea_reconcile_merged_cleanups reported the same worktree safe to remove.

Two independent gaps caused it:

* build_worktree_metadata was never given a pr_number, and only open PRs were
  fetched, so no owning-PR evidence existed at all.
* clean_stale_removable was unreachable for issue_work: it required
  ttl_expired, derived from a last_used_at that nothing populates, and
  is_ttl_expired fail-safes to False when the timestamp is unknown.

This adds deterministic merged-PR linkage and gates removal on the complete
cleanup policy:

* build_pr_index / resolve_owning_pr link a worktree branch to exactly one
  owning PR. Competing PRs on one branch, a still-open owner, a head-branch
  mismatch, or missing PR state all fail closed while still reporting the
  resolved pr_number.
* assess_merged_pr_worktree_cleanup requires all of: conclusive merged
  ownership, branch agreement, containment of the head in authoritative
  master, no open/competing PR, no active lease, no issue lock, no live
  session, a clean tree, and a non-protected checkout. Unknown state blocks.
* Containment reuses merged_cleanup_reconcile.is_head_ancestor_of_ref so the
  audit and the PR-scoped reconciler agree on what "already landed" means.

Lease evidence is now supplied. audit_branches_directory already accepted
leased_branches but the MCP tool never passed it, so has_active_lease was
false for every worktree in a live run. That was inert only while issue
worktrees could never become removable; it is wired to authoritative
control-plane leases here, scoped so a lease on issue N protects that issue's
work worktree and not a baseline or review tree merely named after it.

Issue work no longer becomes removable on TTL age alone, since age is not
proof that a branch landed and would otherwise reclaim a worktree holding
unmerged commits. conflict_fix keeps its existing TTL behaviour, and review,
baseline, merge-simulation, detached, dirty, open-PR, and protected
classifications are unchanged.

The assessor still performs no deletion and gains no cleanup mutation. This
is assessor-side only and does not implement the PR-scoped executor or the
expired-lease reclaim policy tracked separately by #855.

Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>

gitea_mcp_server.py

@@ -11634,6 +11634,7 @@ def gitea_audit_worktree_cleanup(
     org: str | None = None,
     repo: str | None = None,
     ttl_hours: float = worktree_cleanup_audit.DEFAULT_TTL_HOURS,
+    merged_pr_limit: int = 200,
 ) -> dict:
     """Read-only: classify every session-owned worktree under ``branches/`` (#401).
 
@@ -11644,17 +11645,26 @@ def gitea_audit_worktree_cleanup(
     the active issue-lock branch is read from the local lock file and treated
     as active work. Deletes nothing and mutates no Gitea state.
 
-    Fails closed if the live open-PR list cannot be fetched: without it,
-    removability cannot be proven, so no candidates are returned.
+    Merged PRs are fetched as well, so an issue worktree can be linked to the
+    PR that owns its branch (#858). Such a worktree only becomes removable
+    when that owning PR is unambiguous and merged, the worktree head is
+    already contained in authoritative master, and nothing else protects it —
+    no open or competing PR, lease, issue lock, live session, dirty file, or
+    protected/control checkout. Anything unproven keeps it classified as
+    active issue work.
+
+    Fails closed if the live open-PR list, the merged-PR list, or the
+    control-plane lease state cannot be read: without them removability
+    cannot be proven, so no candidates are returned.
 
     Args:
         remote: Known instance — 'dadeschools' or 'prgs'.
         host: Override the Gitea host.
         org: Override the owner/organization.
         repo: Override the repository name.
-        ttl_hours: Age (hours) after which a clean issue/conflict-fix
-            worktree becomes stale-removable (default from
-            GITEA_WORKTREE_TTL_HOURS).
+        ttl_hours: Age (hours) after which a clean conflict-fix worktree
+            becomes stale-removable (default from GITEA_WORKTREE_TTL_HOURS).
+        merged_pr_limit: Max closed PRs scanned for merged-PR ownership.
 
     Returns:
         dict with per-worktree classifications, counts, removable
@@ -11690,22 +11700,84 @@ def gitea_audit_worktree_cleanup(
         if (pr.get("head") or {}).get("ref")
     }
 
+    # #858: merged PRs are the ownership evidence that lets a landed issue
+    # worktree stop being reported as active work. Without them the audit can
+    # never agree with the PR-scoped reconciler, so treat a fetch failure the
+    # same way an open-PR fetch failure is treated: fail closed.
+    try:
+        closed_prs = api_get_all(
+            f"{repo_api_url(h, o, r)}/pulls?state=closed", auth, limit=merged_pr_limit
+        )
+    except Exception as exc:
+        return {
+            "success": False,
+            "performed": False,
+            "open_pr_state_verified": True,
+            "merged_pr_state_verified": False,
+            "reasons": [
+                "could not fetch merged PRs; worktree ownership unverified "
+                f"(fail closed): {_redact(str(exc))}"
+            ],
+        }
+    merged_prs = [pr for pr in closed_prs if (pr.get("merged") or pr.get("merged_at"))]
+    pr_index = worktree_cleanup_audit.build_pr_index(list(open_prs) + merged_prs)
+
+    # #858: the auditor already accepted lease evidence but nothing ever
+    # supplied it, so every worktree looked unleased. Removability is now
+    # reachable for issue worktrees, so authoritative control-plane leases
+    # must be readable or the audit fails closed.
+    db, lease_errs = _control_plane_db_or_error()
+    if db is None:
+        return {
+            "success": False,
+            "performed": False,
+            "open_pr_state_verified": True,
+            "merged_pr_state_verified": True,
+            "lease_state_verified": False,
+            "reasons": [
+                "could not read control-plane leases; worktree protection "
+                "unverified (fail closed)",
+                *lease_errs,
+            ],
+        }
+    lease_result = lease_lifecycle.list_active_leases(
+        db, remote=remote, org=o, repo=r, include_non_active=False, limit=500
+    )
+    leased_issue_numbers: set[int] = set()
+    live_session_paths: set[str] = set()
+    for lease in lease_result.get("leases") or []:
+        if lease.get("work_kind") == "issue" and lease.get("work_number") is not None:
+            try:
+                leased_issue_numbers.add(int(lease["work_number"]))
+            except (TypeError, ValueError):
+                pass
+        if lease.get("worktree_path"):
+            live_session_paths.add(str(lease["worktree_path"]))
+
     active_issue_branches: set[str] = set()
     lock = merged_cleanup_reconcile.read_issue_lock(ISSUE_LOCK_FILE)
     if lock and lock.get("branch_name"):
         active_issue_branches.add(str(lock["branch_name"]).strip())
 
+    master_ref = f"{remote}/master" if remote in REMOTES else "origin/master"
     report = worktree_cleanup_audit.audit_branches_directory(
         _canonical_local_git_root(),
         open_pr_branches=open_pr_branches,
         active_issue_branches=active_issue_branches,
         now=datetime.now(timezone.utc),
         ttl_hours=ttl_hours,
+        pr_index=pr_index,
+        leased_issue_numbers=leased_issue_numbers,
+        live_session_paths=live_session_paths,
+        master_ref=master_ref,
     )
     return {
         "success": True,
         "performed": False,
         "open_pr_state_verified": True,
+        "merged_pr_state_verified": True,
+        "lease_state_verified": True,
+        "master_ref": master_ref,
         "task_mode": "work-issue",
         **report,
     }

tests/test_issue_858_audit_merged_pr_aware.py

@@ -0,0 +1,551 @@
+"""Merged-PR awareness for the worktree cleanup audit (#858).
+
+Before #858 an ``issue_work`` worktree could never leave ``active_issue_work``:
+the audit had no PR linkage at all (``pr_number`` was structurally ``None``)
+and its only route to ``clean_stale_removable`` was a TTL derived from a
+``last_used_at`` that nothing ever populated. A merged, clean, unprotected
+worktree was therefore reported as active work forever, disagreeing with the
+PR-scoped reconciler.
+
+These tests use fabricated temporary repositories and synthetic PR records
+only. Nothing here removes a worktree or deletes a branch.
+"""
+
+import os
+import subprocess
+import sys
+import tempfile
+import unittest
+from unittest.mock import patch
+
+sys.path.insert(0, str(__import__("pathlib").Path(__file__).resolve().parent.parent))
+
+import merged_cleanup_reconcile as mcr  # noqa: E402
+import worktree_cleanup_audit as wca  # noqa: E402
+
+
+MERGED_BRANCH = "feat/issue-777-timeline"
+MERGED_PATH = "/repo/branches/issue-777-timeline"
+HEAD_SHA = "a" * 40
+
+
+def _pr(number, branch, *, merged=True, sha=HEAD_SHA, state=None):
+    """Synthetic Gitea PR payload."""
+    return {
+        "number": number,
+        "head": {"ref": branch, "sha": sha},
+        "merged_at": "2026-07-24T01:00:00Z" if merged else None,
+        "state": state or ("closed" if merged else "open"),
+    }
+
+
+def _porcelain(*entries):
+    out = []
+    for path, branch, sha in entries:
+        out.append(f"worktree {path}")
+        out.append(f"HEAD {sha}")
+        if branch is None:
+            out.append("detached")
+        else:
+            out.append(f"branch refs/heads/{branch}")
+        out.append("")
+    return "\n".join(out)
+
+
+class _AuditHarness(unittest.TestCase):
+    """Runs audit_branches_directory over a fabricated worktree listing."""
+
+    PORCELAIN = _porcelain(
+        ("/repo", "master", "f" * 40),
+        (MERGED_PATH, MERGED_BRANCH, HEAD_SHA),
+    )
+
+    def run_audit(self, *, dirty_paths=(), contained=True, **kwargs):
+        def fake_dirty(path):
+            if path in dirty_paths:
+                return {"exists": True, "dirty": True, "dirty_files": [" M x.py"]}
+            return {"exists": True, "dirty": False, "dirty_files": []}
+
+        with patch.object(
+            wca, "list_worktrees",
+            return_value=wca.parse_worktree_porcelain(self.PORCELAIN),
+        ), patch.object(
+            wca, "read_worktree_dirty", side_effect=fake_dirty
+        ), patch.object(
+            wca, "git_worktree_list", return_value="(mocked)"
+        ), patch.object(
+            wca, "is_head_ancestor_of_ref", return_value=contained
+        ):
+            report = wca.audit_branches_directory("/repo", **kwargs)
+        return {wt["path"]: wt for wt in report["worktrees"]}, report
+
+    def merged_audit(self, **kwargs):
+        kwargs.setdefault("pr_index", wca.build_pr_index([_pr(849, MERGED_BRANCH)]))
+        kwargs.setdefault("master_ref", "prgs/master")
+        return self.run_audit(**kwargs)
+
+
+class TestMergedWorktreeBecomesRemovable(_AuditHarness):
+    def test_clean_merged_issue_worktree_is_linked_and_removable(self):
+        by_path, report = self.merged_audit()
+        entry = by_path[MERGED_PATH]
+
+        self.assertEqual(entry["classification"], wca.CLASS_CLEAN_STALE_REMOVABLE)
+        self.assertTrue(entry["removable"])
+        self.assertEqual(entry["merged_pr_linkage"]["status"], wca.LINKAGE_MERGED)
+        self.assertEqual(entry["merged_pr_cleanup"]["block_reasons"], [])
+        self.assertIn(MERGED_PATH, [c["path"] for c in report["removable_candidates"]])
+
+    def test_pr_number_populated_from_authoritative_linkage(self):
+        by_path, _ = self.merged_audit()
+        self.assertEqual(by_path[MERGED_PATH]["pr_number"], 849)
+
+    def test_regression_without_pr_evidence_stays_active_issue_work(self):
+        """The pre-#858 behaviour, still correct when no PR state is supplied."""
+        by_path, _ = self.run_audit()
+        entry = by_path[MERGED_PATH]
+        self.assertEqual(entry["classification"], wca.CLASS_ACTIVE_ISSUE_WORK)
+        self.assertFalse(entry["removable"])
+        self.assertIsNone(entry["pr_number"])
+
+
+class TestProtectiveSignalsSurvive(_AuditHarness):
+    def test_open_pr_worktree_is_not_removable(self):
+        index = wca.build_pr_index([_pr(900, MERGED_BRANCH, merged=False)])
+        by_path, _ = self.run_audit(
+            pr_index=index,
+            master_ref="prgs/master",
+            open_pr_branches={MERGED_BRANCH},
+        )
+        entry = by_path[MERGED_PATH]
+        self.assertEqual(entry["classification"], wca.CLASS_ACTIVE_OPEN_PR)
+        self.assertFalse(entry["removable"])
+        # linkage still reports the owning PR, it just is not merge proof
+        self.assertEqual(entry["merged_pr_linkage"]["status"], wca.LINKAGE_OPEN)
+        self.assertEqual(entry["pr_number"], 900)
+
+    def test_dirty_tracked_worktree_is_not_removable(self):
+        by_path, _ = self.merged_audit(dirty_paths=(MERGED_PATH,))
+        entry = by_path[MERGED_PATH]
+        self.assertEqual(entry["classification"], wca.CLASS_DIRTY_LOCAL)
+        self.assertFalse(entry["removable"])
+        self.assertIn(
+            "worktree has uncommitted changes",
+            entry["merged_pr_cleanup"]["block_reasons"],
+        )
+
+    def test_untracked_only_worktree_is_not_removable(self):
+        """``git status --porcelain`` reports untracked files as dirty too."""
+        def untracked(path):
+            if path == MERGED_PATH:
+                return {"exists": True, "dirty": True, "dirty_files": ["?? scratch.txt"]}
+            return {"exists": True, "dirty": False, "dirty_files": []}
+
+        with patch.object(
+            wca, "list_worktrees",
+            return_value=wca.parse_worktree_porcelain(self.PORCELAIN),
+        ), patch.object(
+            wca, "read_worktree_dirty", side_effect=untracked
+        ), patch.object(
+            wca, "git_worktree_list", return_value="(mocked)"
+        ), patch.object(
+            wca, "is_head_ancestor_of_ref", return_value=True
+        ):
+            report = wca.audit_branches_directory(
+                "/repo",
+                pr_index=wca.build_pr_index([_pr(849, MERGED_BRANCH)]),
+                master_ref="prgs/master",
+            )
+        entry = {wt["path"]: wt for wt in report["worktrees"]}[MERGED_PATH]
+        self.assertEqual(entry["classification"], wca.CLASS_DIRTY_LOCAL)
+        self.assertFalse(entry["removable"])
+
+    def test_active_lease_by_issue_number_is_protective(self):
+        by_path, _ = self.merged_audit(leased_issue_numbers={777})
+        entry = by_path[MERGED_PATH]
+        self.assertTrue(entry["has_active_lease"])
+        self.assertEqual(entry["classification"], wca.CLASS_ACTIVE_ISSUE_WORK)
+        self.assertFalse(entry["removable"])
+
+    def test_active_lease_by_branch_is_protective(self):
+        by_path, _ = self.merged_audit(leased_branches={MERGED_BRANCH})
+        entry = by_path[MERGED_PATH]
+        self.assertTrue(entry["has_active_lease"])
+        self.assertFalse(entry["removable"])
+
+    def test_active_issue_lock_is_protective(self):
+        by_path, _ = self.merged_audit(active_issue_branches={MERGED_BRANCH})
+        entry = by_path[MERGED_PATH]
+        self.assertTrue(entry["has_active_issue_lock"])
+        self.assertEqual(entry["classification"], wca.CLASS_ACTIVE_ISSUE_WORK)
+        self.assertFalse(entry["removable"])
+
+    def test_live_session_worktree_is_protective(self):
+        by_path, _ = self.merged_audit(live_session_paths={MERGED_PATH})
+        entry = by_path[MERGED_PATH]
+        self.assertTrue(entry["has_live_session"])
+        self.assertEqual(entry["classification"], wca.CLASS_ACTIVE_ISSUE_WORK)
+        self.assertFalse(entry["removable"])
+
+    def test_head_not_contained_in_master_is_not_removable(self):
+        by_path, _ = self.merged_audit(contained=False)
+        entry = by_path[MERGED_PATH]
+        self.assertEqual(entry["classification"], wca.CLASS_ACTIVE_ISSUE_WORK)
+        self.assertFalse(entry["removable"])
+        self.assertIn(
+            "worktree head is not contained in authoritative master "
+            "(unmerged commits remain)",
+            entry["merged_pr_cleanup"]["block_reasons"],
+        )
+
+    def test_unknown_containment_fails_closed(self):
+        by_path, _ = self.merged_audit(contained=None)
+        entry = by_path[MERGED_PATH]
+        self.assertFalse(entry["removable"])
+        self.assertIn(
+            "containment of the worktree head in master is unknown",
+            entry["merged_pr_cleanup"]["block_reasons"],
+        )
+
+    def test_missing_master_ref_fails_closed(self):
+        by_path, _ = self.run_audit(
+            pr_index=wca.build_pr_index([_pr(849, MERGED_BRANCH)])
+        )
+        self.assertFalse(by_path[MERGED_PATH]["removable"])
+
+    def test_unmerged_owning_pr_is_not_removable(self):
+        index = wca.build_pr_index([_pr(901, MERGED_BRANCH, merged=False)])
+        by_path, _ = self.run_audit(pr_index=index, master_ref="prgs/master")
+        entry = by_path[MERGED_PATH]
+        self.assertFalse(entry["removable"])
+        self.assertIn(
+            "owning PR #901 is not merged",
+            entry["merged_pr_cleanup"]["block_reasons"],
+        )
+
+    def test_control_checkout_is_never_removable(self):
+        by_path, _ = self.merged_audit()
+        control = by_path["/repo"]
+        self.assertTrue(control["is_protected"])
+        self.assertEqual(control["classification"], wca.CLASS_UNSAFE_UNKNOWN)
+        self.assertFalse(control["removable"])
+
+    def test_control_checkout_not_removable_even_if_linked_and_merged(self):
+        """A merged PR on the control checkout must not unlock removal."""
+        porcelain = _porcelain(("/repo", MERGED_BRANCH, HEAD_SHA))
+        with patch.object(
+            wca, "list_worktrees", return_value=wca.parse_worktree_porcelain(porcelain)
+        ), patch.object(
+            wca, "read_worktree_dirty",
+            return_value={"exists": True, "dirty": False, "dirty_files": []},
+        ), patch.object(
+            wca, "git_worktree_list", return_value="(mocked)"
+        ), patch.object(
+            wca, "is_head_ancestor_of_ref", return_value=True
+        ):
+            report = wca.audit_branches_directory(
+                "/repo",
+                pr_index=wca.build_pr_index([_pr(849, MERGED_BRANCH)]),
+                master_ref="prgs/master",
+            )
+        entry = report["worktrees"][0]
+        self.assertEqual(entry["classification"], wca.CLASS_UNSAFE_UNKNOWN)
+        self.assertFalse(entry["removable"])
+
+
+class TestAmbiguousLinkageFailsClosed(_AuditHarness):
+    def test_competing_prs_on_one_branch_fail_closed(self):
+        index = wca.build_pr_index(
+            [_pr(849, MERGED_BRANCH), _pr(860, MERGED_BRANCH)]
+        )
+        by_path, _ = self.run_audit(pr_index=index, master_ref="prgs/master")
+        entry = by_path[MERGED_PATH]
+        self.assertEqual(entry["merged_pr_linkage"]["status"], wca.LINKAGE_AMBIGUOUS)
+        self.assertIsNone(entry["pr_number"])
+        self.assertEqual(entry["classification"], wca.CLASS_ACTIVE_ISSUE_WORK)
+        self.assertFalse(entry["removable"])
+
+    def test_merged_plus_open_pr_on_one_branch_fails_closed(self):
+        index = wca.build_pr_index(
+            [_pr(849, MERGED_BRANCH), _pr(861, MERGED_BRANCH, merged=False)]
+        )
+        by_path, _ = self.run_audit(pr_index=index, master_ref="prgs/master")
+        entry = by_path[MERGED_PATH]
+        self.assertEqual(entry["merged_pr_linkage"]["status"], wca.LINKAGE_AMBIGUOUS)
+        self.assertFalse(entry["removable"])
+
+    def test_no_owning_pr_fails_closed(self):
+        by_path, _ = self.run_audit(
+            pr_index=wca.build_pr_index([_pr(849, "feat/other-branch")]),
+            master_ref="prgs/master",
+        )
+        entry = by_path[MERGED_PATH]
+        self.assertEqual(entry["merged_pr_linkage"]["status"], wca.LINKAGE_NONE)
+        self.assertFalse(entry["removable"])
+
+    def test_malformed_pr_records_are_dropped_not_guessed(self):
+        index = wca.build_pr_index(
+            [
+                {"number": None, "head": {"ref": MERGED_BRANCH}},
+                {"number": 5, "head": {}},
+                {"number": "not-an-int", "head": {"ref": MERGED_BRANCH}},
+            ]
+        )
+        self.assertEqual(index, {})
+        self.assertEqual(
+            wca.resolve_owning_pr(branch=MERGED_BRANCH, pr_index=index)["status"],
+            wca.LINKAGE_NONE,
+        )
+
+    def test_detached_worktree_has_no_branch_linkage(self):
+        self.assertEqual(
+            wca.resolve_owning_pr(branch=None, pr_index={})["status"],
+            wca.LINKAGE_UNKNOWN,
+        )
+
+
+class TestUnrelatedClassificationsUnchanged(unittest.TestCase):
+    """Non-issue_work worktrees keep their pre-#858 classifications."""
+
+    PORCELAIN = _porcelain(
+        ("/repo", "master", "f" * 40),
+        ("/repo/branches/review-pr42", "review-pr42", "2" * 40),
+        ("/repo/branches/baseline-master-x", "baseline-master-x", "3" * 40),
+        ("/repo/branches/conflict-fix-pr50", "conflict-fix-pr50", "4" * 40),
+        ("/repo/branches/review-pr99", None, "5" * 40),
+    )
+
+    def _audit(self, **kwargs):
+        with patch.object(
+            wca, "list_worktrees",
+            return_value=wca.parse_worktree_porcelain(self.PORCELAIN),
+        ), patch.object(
+            wca, "read_worktree_dirty",
+            return_value={"exists": True, "dirty": False, "dirty_files": []},
+        ), patch.object(
+            wca, "git_worktree_list", return_value="(mocked)"
+        ), patch.object(
+            wca, "is_head_ancestor_of_ref", return_value=True
+        ):
+            report = wca.audit_branches_directory("/repo", **kwargs)
+        return {wt["path"]: wt for wt in report["worktrees"]}
+
+    def test_classifications_identical_with_and_without_pr_evidence(self):
+        without = self._audit()
+        with_evidence = self._audit(
+            pr_index=wca.build_pr_index([_pr(849, MERGED_BRANCH)]),
+            master_ref="prgs/master",
+        )
+        self.assertEqual(
+            {p: e["classification"] for p, e in without.items()},
+            {p: e["classification"] for p, e in with_evidence.items()},
+        )
+
+    def test_lease_on_issue_does_not_capture_similarly_named_scratch_trees(self):
+        """A lease on issue 777 protects issue work, not baseline/review trees."""
+        porcelain = _porcelain(
+            ("/repo/branches/baseline-master-issue-777", "baseline-issue-777", "7" * 40),
+            ("/repo/branches/issue-777-timeline", MERGED_BRANCH, HEAD_SHA),
+        )
+        with patch.object(
+            wca, "list_worktrees", return_value=wca.parse_worktree_porcelain(porcelain)
+        ), patch.object(
+            wca, "read_worktree_dirty",
+            return_value={"exists": True, "dirty": False, "dirty_files": []},
+        ), patch.object(
+            wca, "git_worktree_list", return_value="(mocked)"
+        ), patch.object(
+            wca, "is_head_ancestor_of_ref", return_value=True
+        ):
+            report = wca.audit_branches_directory(
+                "/repo",
+                pr_index=wca.build_pr_index([_pr(849, MERGED_BRANCH)]),
+                master_ref="prgs/master",
+                leased_issue_numbers={777},
+            )
+        by_path = {wt["path"]: wt for wt in report["worktrees"]}
+
+        baseline = by_path["/repo/branches/baseline-master-issue-777"]
+        self.assertFalse(baseline["has_active_lease"])
+        self.assertEqual(baseline["classification"], wca.CLASS_CLEAN_STALE_REMOVABLE)
+
+        issue_work = by_path["/repo/branches/issue-777-timeline"]
+        self.assertTrue(issue_work["has_active_lease"])
+        self.assertFalse(issue_work["removable"])
+
+    def test_review_and_baseline_still_removable(self):
+        by_path = self._audit(
+            pr_index=wca.build_pr_index([]), master_ref="prgs/master"
+        )
+        self.assertEqual(
+            by_path["/repo/branches/review-pr42"]["classification"],
+            wca.CLASS_CLEAN_STALE_REMOVABLE,
+        )
+        self.assertEqual(
+            by_path["/repo/branches/baseline-master-x"]["classification"],
+            wca.CLASS_CLEAN_STALE_REMOVABLE,
+        )
+        self.assertEqual(
+            by_path["/repo/branches/review-pr99"]["classification"],
+            wca.CLASS_DETACHED_REVIEW_LEFTOVER,
+        )
+
+    def test_conflict_fix_ttl_behaviour_unchanged(self):
+        """conflict_fix still needs only TTL expiry; #858 did not touch it."""
+        self.assertEqual(
+            wca.classify_worktree(
+                workflow_type=wca.WORKFLOW_CONFLICT_FIX,
+                is_dirty=False,
+                ttl_expired=True,
+            ),
+            wca.CLASS_CLEAN_STALE_REMOVABLE,
+        )
+        self.assertEqual(
+            wca.classify_worktree(
+                workflow_type=wca.WORKFLOW_CONFLICT_FIX,
+                is_dirty=False,
+                ttl_expired=False,
+            ),
+            wca.CLASS_ACTIVE_ISSUE_WORK,
+        )
+
+    def test_issue_work_ttl_alone_no_longer_grants_removal(self):
+        """Age is not landing proof: TTL alone must not reclaim issue work."""
+        self.assertEqual(
+            wca.classify_worktree(
+                workflow_type=wca.WORKFLOW_ISSUE_WORK,
+                is_dirty=False,
+                ttl_expired=True,
+            ),
+            wca.CLASS_ACTIVE_ISSUE_WORK,
+        )
+
+
+class TestAssessorPerformsNoDeletion(_AuditHarness):
+    def test_audit_never_removes_a_worktree(self):
+        with patch.object(wca, "remove_worktree") as removal:
+            self.merged_audit()
+        removal.assert_not_called()
+
+    def test_audit_shells_out_to_no_destructive_git_command(self):
+        seen = []
+        real_run = subprocess.run
+
+        def recording_run(cmd, *args, **kwargs):
+            seen.append(cmd)
+            return real_run(["true"], *args, **kwargs)
+
+        with patch.object(subprocess, "run", side_effect=recording_run):
+            wca.audit_branches_directory("/nonexistent-repo-for-audit")
+
+        joined = [" ".join(c) if isinstance(c, list) else str(c) for c in seen]
+        for cmd in joined:
+            self.assertNotIn("worktree remove", cmd)
+            self.assertNotIn("branch -D", cmd)
+            self.assertNotIn("push", cmd)
+
+
+class TestAgreementWithPrScopedReconciler(unittest.TestCase):
+    """The audit and merged_cleanup_reconcile must agree on identical input.
+
+    Uses a real throwaway git repository so containment is computed by git
+    rather than asserted. Nothing outside the temporary directory is touched.
+    """
+
+    def _git(self, *args):
+        subprocess.run(
+            ["git", "-C", self.root, *args],
+            check=True,
+            capture_output=True,
+            text=True,
+        )
+
+    def setUp(self):
+        self._tmp = tempfile.TemporaryDirectory()
+        self.root = os.path.realpath(self._tmp.name)
+        self._git("init", "-b", "master", ".")
+        self._git("config", "user.email", "[email protected]")
+        self._git("config", "user.name", "Test")
+        with open(os.path.join(self.root, "seed.txt"), "w") as fh:
+            fh.write("seed\n")
+        self._git("add", "seed.txt")
+        self._git("commit", "-m", "seed")
+
+        self.branch = "feat/issue-777-timeline"
+        self._git("checkout", "-b", self.branch)
+        with open(os.path.join(self.root, "feature.txt"), "w") as fh:
+            fh.write("feature\n")
+        self._git("add", "feature.txt")
+        self._git("commit", "-m", "feature")
+        self.head_sha = subprocess.run(
+            ["git", "-C", self.root, "rev-parse", "HEAD"],
+            capture_output=True, text=True, check=True,
+        ).stdout.strip()
+        self._git("checkout", "master")
+        self._git("merge", "--no-ff", "-m", "merge feature", self.branch)
+
+        self.worktree = os.path.join(self.root, "branches", "issue-777-timeline")
+        self._git("worktree", "add", self.worktree, self.branch)
+
+    def tearDown(self):
+        self._tmp.cleanup()
+
+    def _pr_index(self):
+        return wca.build_pr_index(
+            [
+                {
+                    "number": 849,
+                    "head": {"ref": self.branch, "sha": self.head_sha},
+                    "merged_at": "2026-07-24T01:00:00Z",
+                }
+            ]
+        )
+
+    def _audit_entry(self):
+        report = wca.audit_branches_directory(
+            self.root, pr_index=self._pr_index(), master_ref="master"
+        )
+        return next(wt for wt in report["worktrees"] if wt["path"] == self.worktree)
+
+    def _reconciler_entry(self):
+        return mcr.assess_local_worktree_cleanup(
+            pr_number=849,
+            head_branch=self.branch,
+            merged=True,
+            worktree_state=mcr.resolve_cleanup_worktree_state(
+                project_root=self.root,
+                head_branch=self.branch,
+                issue_number=777,
+                pr_head_sha=self.head_sha,
+                target_ref="master",
+            ),
+            active_lock=False,
+        )
+
+    def test_both_assessors_agree_the_worktree_is_safe(self):
+        audit_entry = self._audit_entry()
+        reconciler = self._reconciler_entry()
+
+        self.assertTrue(reconciler["safe_to_remove_worktree"], reconciler)
+        self.assertTrue(audit_entry["removable"], audit_entry)
+        self.assertEqual(audit_entry["pr_number"], reconciler["pr_number"])
+        self.assertEqual(audit_entry["merged_pr_cleanup"]["block_reasons"], [])
+        self.assertEqual(reconciler["block_reasons"], [])
+
+    def test_both_assessors_agree_a_dirty_worktree_is_unsafe(self):
+        with open(os.path.join(self.worktree, "feature.txt"), "a") as fh:
+            fh.write("local edit\n")
+
+        audit_entry = self._audit_entry()
+        reconciler = self._reconciler_entry()
+
+        self.assertFalse(audit_entry["removable"])
+        self.assertFalse(reconciler["safe_to_remove_worktree"])
+
+    def test_worktree_still_present_after_audit(self):
+        self._audit_entry()
+        self.assertTrue(os.path.isdir(self.worktree))
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_worktree_cleanup_audit.py

@@ -134,13 +134,35 @@ class TestClassification(unittest.TestCase):
         self.assertEqual(cls, wca.CLASS_ACTIVE_OPEN_PR)
         self.assertFalse(wca.is_removable(cls))
 
-    def test_stale_clean_issue_worktree_removable(self):
-        # Scenario 5: clean issue worktree, TTL expired, no lock -> removable.
+    def test_stale_clean_issue_worktree_needs_merged_pr_proof(self):
+        # Scenario 5 (#858): age is not proof that the branch landed, so a
+        # TTL-expired issue worktree stays active work. Only authoritative
+        # merged-PR evidence makes it removable, which is what keeps a
+        # worktree holding unmerged commits from being reclaimed by age.
         cls = wca.classify_worktree(
             workflow_type=wca.WORKFLOW_ISSUE_WORK,
             is_dirty=False,
             ttl_expired=True,
         )
+        self.assertEqual(cls, wca.CLASS_ACTIVE_ISSUE_WORK)
+        self.assertFalse(wca.is_removable(cls))
+
+        cls = wca.classify_worktree(
+            workflow_type=wca.WORKFLOW_ISSUE_WORK,
+            is_dirty=False,
+            ttl_expired=True,
+            merged_pr_cleanup={"proven": True},
+        )
+        self.assertEqual(cls, wca.CLASS_CLEAN_STALE_REMOVABLE)
+        self.assertTrue(wca.is_removable(cls))
+
+    def test_stale_clean_conflict_fix_worktree_removable(self):
+        # conflict_fix keeps the original TTL rule; #858 changed issue work only.
+        cls = wca.classify_worktree(
+            workflow_type=wca.WORKFLOW_CONFLICT_FIX,
+            is_dirty=False,
+            ttl_expired=True,
+        )
         self.assertEqual(cls, wca.CLASS_CLEAN_STALE_REMOVABLE)
         self.assertTrue(wca.is_removable(cls))
 

worktree_cleanup_audit.py

@@ -34,7 +34,11 @@ import subprocess
 from datetime import datetime, timezone
 from typing import Any
 
-from merged_cleanup_reconcile import branch_worktree_folder, read_local_worktree_state
+from merged_cleanup_reconcile import (
+    branch_worktree_folder,
+    is_head_ancestor_of_ref,
+    read_local_worktree_state,
+)
 from reviewer_worktree import parse_dirty_tracked_files, REVIEW_WORKTREE_RE
 
 PROTECTED_BRANCHES = frozenset({"master", "main", "dev"})
@@ -67,6 +71,14 @@ REMOVABLE_CLASSES = frozenset(
     {CLASS_CLEAN_STALE_REMOVABLE, CLASS_DETACHED_REVIEW_LEFTOVER}
 )
 
+# Merged-PR linkage outcomes for issue worktrees (#858). Only ``LINKAGE_MERGED``
+# is ownership proof; every other outcome leaves the worktree protected.
+LINKAGE_MERGED = "merged_pr"
+LINKAGE_OPEN = "open_pr"
+LINKAGE_NONE = "no_owning_pr"
+LINKAGE_AMBIGUOUS = "ambiguous"
+LINKAGE_UNKNOWN = "unknown"
+
 _ISSUE_REF_RE = re.compile(r"issue-(\d+)", re.IGNORECASE)
 _ISSUE_BRANCH_PREFIXES = ("feat/", "fix/", "docs/", "chore/")
 
@@ -169,6 +181,186 @@ def is_ttl_expired(
     return (now_dt - last).total_seconds() > ttl_hours * 3600.0
 
 
+def build_pr_index(prs: list[dict[str, Any]] | None) -> dict[str, list[dict[str, Any]]]:
+    """Index PR records by head branch for deterministic worktree linkage (#858).
+
+    Accepts Gitea PR payloads (``head`` as a dict) and pre-flattened records
+    (``head_branch``/``head_sha``). Records without a usable head branch or
+    number are dropped rather than guessed at, so a branch is only ever linked
+    to a PR the caller actually proved.
+    """
+    index: dict[str, list[dict[str, Any]]] = {}
+    for pr in prs or []:
+        head = pr.get("head")
+        if isinstance(head, dict):
+            head_branch = head.get("ref")
+            head_sha = head.get("sha")
+        else:
+            head_branch = pr.get("head_branch") or (head if isinstance(head, str) else None)
+            head_sha = pr.get("head_sha")
+        number = pr.get("number")
+        if not head_branch or number is None:
+            continue
+        try:
+            pr_number = int(number)
+        except (TypeError, ValueError):
+            continue
+        index.setdefault(str(head_branch).strip(), []).append(
+            {
+                "pr_number": pr_number,
+                "head_branch": str(head_branch).strip(),
+                "head_sha": head_sha,
+                "merged": bool(pr.get("merged") or pr.get("merged_at")),
+                "state": pr.get("state"),
+            }
+        )
+    return index
+
+
+def resolve_owning_pr(
+    *,
+    branch: str | None,
+    pr_index: dict[str, list[dict[str, Any]]] | None,
+) -> dict[str, Any]:
+    """Resolve the single PR that owns ``branch``, failing closed when unclear.
+
+    Ownership is only ``LINKAGE_MERGED`` when exactly one PR claims the branch
+    and that PR is merged. Several distinct PRs on one branch is a competing
+    claim (``LINKAGE_AMBIGUOUS``), and a still-open owner is reported as
+    ``LINKAGE_OPEN`` — both keep the worktree protected while still exposing
+    the PR number the audit resolved.
+    """
+    if pr_index is None:
+        return {
+            "status": LINKAGE_UNKNOWN,
+            "pr_number": None,
+            "candidate_pr_numbers": [],
+            "reasons": ["live PR state was not supplied; ownership unproven"],
+        }
+    branch_name = (branch or "").strip()
+    if not branch_name:
+        return {
+            "status": LINKAGE_UNKNOWN,
+            "pr_number": None,
+            "candidate_pr_numbers": [],
+            "reasons": ["worktree has no attached branch; ownership unproven"],
+        }
+
+    candidates = list(pr_index.get(branch_name) or [])
+    numbers = sorted({c["pr_number"] for c in candidates})
+    if not candidates:
+        return {
+            "status": LINKAGE_NONE,
+            "pr_number": None,
+            "candidate_pr_numbers": [],
+            "reasons": [f"no PR claims branch '{branch_name}'"],
+        }
+    if len(numbers) > 1:
+        return {
+            "status": LINKAGE_AMBIGUOUS,
+            "pr_number": None,
+            "candidate_pr_numbers": numbers,
+            "reasons": [
+                f"branch '{branch_name}' is claimed by competing PRs {numbers}; "
+                "ownership is ambiguous"
+            ],
+        }
+
+    owner = candidates[0]
+    pr_number = owner["pr_number"]
+    if owner.get("head_branch") != branch_name:
+        return {
+            "status": LINKAGE_UNKNOWN,
+            "pr_number": pr_number,
+            "candidate_pr_numbers": numbers,
+            "reasons": [
+                f"PR #{pr_number} head branch '{owner.get('head_branch')}' does not "
+                f"match worktree branch '{branch_name}'"
+            ],
+        }
+    if not owner.get("merged"):
+        return {
+            "status": LINKAGE_OPEN,
+            "pr_number": pr_number,
+            "candidate_pr_numbers": numbers,
+            "pr_head_sha": owner.get("head_sha"),
+            "reasons": [f"owning PR #{pr_number} is not merged"],
+        }
+    return {
+        "status": LINKAGE_MERGED,
+        "pr_number": pr_number,
+        "candidate_pr_numbers": numbers,
+        "pr_head_sha": owner.get("head_sha"),
+        "reasons": [],
+    }
+
+
+def assess_merged_pr_worktree_cleanup(
+    *,
+    linkage: dict[str, Any] | None,
+    head_sha: str | None,
+    head_in_master: bool | None,
+    is_dirty: bool,
+    has_open_pr: bool,
+    has_active_lease: bool,
+    has_active_issue_lock: bool,
+    is_protected: bool,
+    has_live_session: bool = False,
+) -> dict[str, Any]:
+    """Decide whether a merged issue worktree satisfies the full cleanup policy.
+
+    Every condition must be independently proven: conclusive merged-PR
+    ownership, agreement between the worktree branch and the PR head branch,
+    containment of the worktree head in authoritative master (which is what
+    proves no unmerged commits remain), absence of any open/competing PR,
+    lease, issue lock, or live session, a clean tree, and a worktree that is
+    not the protected control checkout. Anything unknown blocks.
+    """
+    link = linkage or {
+        "status": LINKAGE_UNKNOWN,
+        "pr_number": None,
+        "reasons": ["no linkage assessment supplied"],
+    }
+    status = link.get("status")
+    reasons: list[str] = []
+
+    if status != LINKAGE_MERGED:
+        reasons.extend(
+            link.get("reasons") or ["owning PR could not be conclusively identified"]
+        )
+    if is_protected:
+        reasons.append("worktree is protected or the stable control checkout")
+    if is_dirty:
+        reasons.append("worktree has uncommitted changes")
+    if has_open_pr:
+        reasons.append("worktree branch has an open PR")
+    if has_active_lease:
+        reasons.append("worktree has an active lease")
+    if has_active_issue_lock:
+        reasons.append("an active issue lock references this branch")
+    if has_live_session:
+        reasons.append("a live process or session is using this worktree")
+    if not head_sha:
+        reasons.append("worktree head sha is unknown")
+    if head_in_master is None:
+        reasons.append("containment of the worktree head in master is unknown")
+    elif not head_in_master:
+        reasons.append(
+            "worktree head is not contained in authoritative master "
+            "(unmerged commits remain)"
+        )
+
+    proven = not reasons
+    return {
+        "linkage_status": status,
+        "pr_number": link.get("pr_number"),
+        "pr_head_sha": link.get("pr_head_sha"),
+        "head_in_master": head_in_master,
+        "proven": proven,
+        "block_reasons": reasons,
+    }
+
+
 def classify_worktree(
     *,
     workflow_type: str,
@@ -181,6 +373,8 @@ def classify_worktree(
     ttl_expired: bool = False,
     is_protected: bool = False,
     metadata_known: bool = True,
+    merged_pr_cleanup: dict[str, Any] | None = None,
+    has_live_session: bool = False,
 ) -> str:
     """Classify a worktree, safety-first: any preservation signal wins.
 
@@ -199,6 +393,8 @@ def classify_worktree(
         return CLASS_ACTIVE_ISSUE_WORK  # never auto-deleted (criterion 8)
     if has_active_issue_lock:
         return CLASS_ACTIVE_ISSUE_WORK
+    if has_live_session:
+        return CLASS_ACTIVE_ISSUE_WORK  # a live session still owns this tree
     if not metadata_known or workflow_type == WORKFLOW_UNKNOWN:
         return CLASS_UNSAFE_UNKNOWN  # never auto-deleted without proof
 
@@ -207,7 +403,15 @@ def classify_worktree(
         if is_detached or branch_gone:
             return CLASS_DETACHED_REVIEW_LEFTOVER
         return CLASS_CLEAN_STALE_REMOVABLE
-    # issue_work / conflict_fix: only removable once the TTL has expired.
+    if workflow_type == WORKFLOW_ISSUE_WORK:
+        # #858: an issue worktree becomes removable only on authoritative
+        # merged-PR evidence satisfying the whole cleanup policy. Age alone
+        # never proves the branch landed, so TTL cannot qualify one by itself
+        # — otherwise a worktree holding unmerged commits would be reclaimed.
+        if (merged_pr_cleanup or {}).get("proven"):
+            return CLASS_CLEAN_STALE_REMOVABLE
+        return CLASS_ACTIVE_ISSUE_WORK
+    # conflict_fix: only removable once the TTL has expired.
     if ttl_expired:
         return CLASS_CLEAN_STALE_REMOVABLE
     return CLASS_ACTIVE_ISSUE_WORK
@@ -400,6 +604,20 @@ def remove_worktree(project_root: str, path: str) -> dict[str, Any]:
     }
 
 
+def head_contained_in_ref(
+    project_root: str, head_sha: str | None, ref: str | None
+) -> bool | None:
+    """Return True when ``head_sha`` is already contained in ``ref``.
+
+    Shares :mod:`merged_cleanup_reconcile`'s ancestry check so the audit and
+    the PR-scoped reconciler agree on what "already landed" means (#858).
+    Returns None when containment cannot be determined, which fails closed.
+    """
+    if not head_sha or not ref:
+        return None
+    return is_head_ancestor_of_ref(project_root, head_sha, ref)
+
+
 def _is_under_branches(project_root: str, path: str) -> bool:
     branches_root = os.path.join(os.path.abspath(project_root), "branches")
     return os.path.abspath(path or "").startswith(branches_root + os.sep)
@@ -413,16 +631,30 @@ def audit_branches_directory(
     active_issue_branches: set[str] | None = None,
     now: datetime | str | None = None,
     ttl_hours: float = DEFAULT_TTL_HOURS,
+    pr_index: dict[str, list[dict[str, Any]]] | None = None,
+    leased_issue_numbers: set[int] | None = None,
+    live_session_paths: set[str] | None = None,
+    master_ref: str | None = None,
 ) -> dict[str, Any]:
     """Classify every session-owned worktree under ``branches/``.
 
     Read-only: shells out to git for discovery and dirty state, then applies
     the pure classifier. Returns per-worktree classifications, counts, the
     list of removable candidates, and the ``git worktree list`` proof.
+
+    ``pr_index`` (see :func:`build_pr_index`) supplies the authoritative PR
+    ownership used to link issue worktrees to their merged PR (#858).
+    ``master_ref`` is the ref a worktree head must be contained in before it
+    can be considered landed. Both are optional and their absence only ever
+    fails closed: without them no issue worktree becomes removable.
     """
     open_pr_branches = open_pr_branches or set()
     leased_branches = leased_branches or set()
     active_issue_branches = active_issue_branches or set()
+    leased_issue_numbers = leased_issue_numbers or set()
+    live_session_paths = {
+        os.path.abspath(p) for p in (live_session_paths or set()) if p
+    }
 
     worktrees: list[dict[str, Any]] = []
     for entry in list_worktrees(project_root):
@@ -433,12 +665,42 @@ def audit_branches_directory(
         )
         dirty_state = read_worktree_dirty(path)
         is_dirty = bool(dirty_state.get("dirty"))
+        head_sha = entry.get("head")
+        linkage = resolve_owning_pr(branch=branch, pr_index=pr_index)
         metadata = build_worktree_metadata(
-            path=path, branch=branch, head_sha=entry.get("head")
+            path=path,
+            branch=branch,
+            head_sha=head_sha,
+            pr_number=linkage.get("pr_number"),
         )
         has_open_pr = bool(branch) and branch in open_pr_branches
-        has_active_lease = bool(branch) and branch in leased_branches
+        # A lease on issue N protects that issue's own work worktree. It must
+        # not incidentally protect a baseline/review scratch tree that merely
+        # carries the same issue marker in its name, which would change the
+        # classification of worktrees this policy does not own.
+        has_active_lease = (bool(branch) and branch in leased_branches) or (
+            metadata["workflow_type"] == WORKFLOW_ISSUE_WORK
+            and metadata.get("issue_number") is not None
+            and metadata["issue_number"] in leased_issue_numbers
+        )
         has_active_lock = bool(branch) and branch in active_issue_branches
+        has_live_session = bool(path) and os.path.abspath(path) in live_session_paths
+        head_in_master = (
+            head_contained_in_ref(project_root, head_sha, master_ref)
+            if master_ref
+            else None
+        )
+        merged_pr_cleanup = assess_merged_pr_worktree_cleanup(
+            linkage=linkage,
+            head_sha=head_sha,
+            head_in_master=head_in_master,
+            is_dirty=is_dirty,
+            has_open_pr=has_open_pr,
+            has_active_lease=has_active_lease,
+            has_active_issue_lock=has_active_lock,
+            is_protected=is_protected,
+            has_live_session=has_live_session,
+        )
         ttl_expired = is_ttl_expired(
             last_used_at=metadata.get("last_used_at"), now=now, ttl_hours=ttl_hours
         )
@@ -452,6 +714,8 @@ def audit_branches_directory(
             branch_gone=branch is None and not entry.get("detached"),
             ttl_expired=ttl_expired,
             is_protected=is_protected,
+            merged_pr_cleanup=merged_pr_cleanup,
+            has_live_session=has_live_session,
         )
         metadata["cleanup_eligibility"] = classification
         worktrees.append(
@@ -463,7 +727,10 @@ def audit_branches_directory(
                 "has_open_pr": has_open_pr,
                 "has_active_lease": has_active_lease,
                 "has_active_issue_lock": has_active_lock,
+                "has_live_session": has_live_session,
                 "is_protected": is_protected,
+                "merged_pr_linkage": linkage,
+                "merged_pr_cleanup": merged_pr_cleanup,
                 "classification": classification,
                 "removable": is_removable(classification),
             }