docs/llm-workflow-runbooks.md

@@ -344,6 +344,37 @@ explicit control-checkout repair.
 
 Portable wording: [`skills/llm-project-workflow/SKILL.md`](../skills/llm-project-workflow/SKILL.md).
 
+### Root checkout guard (#475)
+
+The MCP server enforces a fail-closed **root checkout guard** before author,
+reviewer, and merger mutations when the active workspace is not an isolated
+`branches/...` worktree (reconciler close paths remain exempt per #468).
+
+The guard blocks when the **control checkout** (repository root) is:
+
+- on a non-stable branch (`master` / `main` / `dev` expected),
+- detached HEAD,
+- dirty (tracked edits),
+- or its `HEAD` does not match `prgs/master` when that ref is available.
+
+**Remediation (never auto-reset or stash):**
+
+> Root checkout is not on master. Preserve state, switch root back to master,
+> and use `scripts/worktree-review` or the sanctioned issue worktree flow.
+
+**Recovery after root hijack:**
+
+1. Preserve any in-progress edits (copy paths, note branch name, or commit on a
+   rescue branch from a `branches/...` worktree).
+2. From the repository root: `git checkout master` (or `main` / `dev` per repo
+   policy) and `git fetch prgs && git merge --ff-only prgs/master` when safe.
+3. Confirm `git status` is clean and `git branch --show-current` is `master`.
+4. Resume work only inside `branches/issue-<n>-<slug>` via `gitea_lock_issue` /
+   `git worktree add`.
+
+`branches/...` directories are disposable role worktrees; the root checkout is
+the stable orchestration surface only.
+
 ## Shell Spawn Hard-Stop Rule
 
 Symptom: a shell tool call returns `exit_code: -1` with empty stdout/stderr.

gitea_mcp_server.py

@@ -507,8 +507,30 @@ def verify_preflight_purity(remote: str | None = None, worktree_path: str | None
                     f"{_format_preflight_files(reviewer_delta)}"
                 )
 
+    _enforce_root_checkout_guard(worktree_path)
     _enforce_branches_only_author_mutation(worktree_path)
 
+
+def _enforce_root_checkout_guard(worktree_path: str | None = None) -> None:
+    """#475: fail closed when the stable control checkout is contaminated."""
+    ctx = _resolve_author_mutation_context(worktree_path)
+    canonical_root = ctx["canonical_repo_root"]
+    workspace = ctx["workspace_path"]
+    git_state = issue_lock_worktree.read_worktree_git_state(canonical_root)
+    remote_master_sha = root_checkout_guard.resolve_remote_master_sha(canonical_root)
+    assessment = root_checkout_guard.assess_root_checkout_guard(
+        workspace_path=workspace,
+        canonical_repo_root=canonical_root,
+        current_branch=git_state.get("current_branch"),
+        head_sha=git_state.get("head_sha"),
+        porcelain_status=git_state.get("porcelain_status") or "",
+        remote_master_sha=remote_master_sha,
+        resolved_role=_preflight_resolved_role,
+    )
+    if assessment["block"]:
+        raise RuntimeError(root_checkout_guard.format_root_checkout_guard_error(assessment))
+
+
 from mcp.server.fastmcp import FastMCP  # noqa: E402
 
 from gitea_auth import (  # noqa: E402
@@ -538,6 +560,7 @@ import issue_lock_adoption  # noqa: E402
 import merge_approval_gate  # noqa: E402
 import already_landed_reconcile  # noqa: E402
 import author_mutation_worktree  # noqa: E402
+import root_checkout_guard  # noqa: E402
 import issue_claim_heartbeat  # noqa: E402
 import issue_work_duplicate_gate  # noqa: E402
 import reviewer_pr_lease  # noqa: E402

root_checkout_guard.py

@@ -0,0 +1,133 @@
+"""Root checkout guard (#475).
+
+The project root checkout is the stable control checkout on master/prgs/master.
+Author/reviewer/merge flows must fail closed when the control checkout is
+contaminated (wrong branch, detached HEAD, dirty, or HEAD behind/ahead of
+prgs/master). Isolated ``branches/...`` worktrees remain allowed.
+"""
+
+from __future__ import annotations
+
+import os
+import subprocess
+
+from author_mutation_worktree import is_path_under_branches
+from reviewer_worktree import parse_dirty_tracked_files
+
+REMEDIATION = (
+    "Root checkout is not on master. Preserve state, switch root back to master, "
+    "and use scripts/worktree-review or the sanctioned issue worktree flow."
+)
+
+BASE_BRANCHES = frozenset({"master", "main", "dev"})
+REMOTE_MASTER_REFS = ("prgs/master", "refs/remotes/prgs/master")
+
+
+def resolve_remote_master_sha(
+    canonical_repo_root: str,
+    *,
+    remote_refs: tuple[str, ...] | None = None,
+) -> str | None:
+    """Return the commit SHA for the tracking master ref when available."""
+    root = (canonical_repo_root or "").strip()
+    if not root:
+        return None
+    for ref in remote_refs or REMOTE_MASTER_REFS:
+        res = subprocess.run(
+            ["git", "-C", root, "rev-parse", "--verify", ref],
+            capture_output=True,
+            text=True,
+            check=False,
+        )
+        if res.returncode == 0:
+            sha = (res.stdout or "").strip()
+            if sha:
+                return sha
+    return None
+
+
+resolve_tracking_master_sha = resolve_remote_master_sha
+
+
+def assess_root_checkout_guard(
+    *,
+    workspace_path: str,
+    canonical_repo_root: str,
+    current_branch: str | None,
+    head_sha: str | None,
+    porcelain_status: str,
+    remote_master_sha: str | None,
+    resolved_role: str | None = None,
+) -> dict:
+    """Fail closed when the control checkout is not clean master/prgs/master."""
+    reasons: list[str] = []
+    root = os.path.realpath(canonical_repo_root)
+    workspace = os.path.realpath(workspace_path)
+    branch = (current_branch or "").strip()
+    dirty_files = parse_dirty_tracked_files(porcelain_status)
+
+    if resolved_role == "reconciler":
+        return _assessment(True, [], root, workspace, branch, head_sha, dirty_files)
+
+    if resolved_role != "merger" and is_path_under_branches(workspace, root):
+        return _assessment(True, [], root, workspace, branch, head_sha, dirty_files)
+
+    if dirty_files:
+        reasons.append(
+            "control checkout has tracked local edits before role work "
+            f"(dirty files: {', '.join(dirty_files)})"
+        )
+
+    if not branch:
+        reasons.append("control checkout is detached HEAD; expected branch 'master'")
+    elif branch not in BASE_BRANCHES:
+        reasons.append(
+            f"control checkout branch '{branch}' is not a stable base branch "
+            f"({'/'.join(sorted(BASE_BRANCHES))})"
+        )
+
+    if remote_master_sha and head_sha and head_sha != remote_master_sha:
+        reasons.append(
+            "control checkout HEAD does not match prgs/master "
+            f"(HEAD {head_sha[:12]}, prgs/master {remote_master_sha[:12]})"
+        )
+
+    proven = not reasons
+    return _assessment(proven, reasons, root, workspace, branch or None, head_sha, dirty_files)
+
+
+def format_root_checkout_guard_error(assessment: dict) -> str:
+    """Single RuntimeError message for MCP preflight gates."""
+    root = assessment.get("canonical_repo_root") or "(unknown)"
+    workspace = assessment.get("workspace_path") or "(unknown)"
+    reasons = "; ".join(assessment.get("reasons") or ["unknown root checkout violation"])
+    return (
+        f"Root checkout guard (#475): {reasons}. "
+        f"canonical repository root: {root}; workspace: {workspace}. "
+        f"{REMEDIATION}"
+    )
+
+
+def _assessment(
+    proven: bool,
+    reasons: list[str],
+    canonical_repo_root: str,
+    workspace_path: str,
+    current_branch: str | None,
+    head_sha: str | None,
+    dirty_files: list[str],
+) -> dict:
+    return {
+        "proven": proven,
+        "block": not proven,
+        "reasons": reasons,
+        "canonical_repo_root": canonical_repo_root,
+        "workspace_path": workspace_path,
+        "current_branch": current_branch,
+        "head_sha": head_sha,
+        "dirty_files": dirty_files,
+        "remediation": REMEDIATION,
+    }
+
+
+assess_root_checkout = assess_root_checkout_guard

tests/test_create_issue_workspace_guard.py

@@ -38,8 +38,18 @@ class TestCreateIssueWorkspaceGuard(unittest.TestCase):
     @patch("gitea_mcp_server.role_session_router.check_author_mutation_after_reviewer_stop", return_value=(True, []))
     @patch("gitea_mcp_server.api_request")
     @patch("gitea_mcp_server.api_get_all", return_value=[])
-    @patch("gitea_mcp_server.issue_lock_worktree.read_worktree_git_state", return_value={"current_branch": "feat/issue-1"})
+    @patch("gitea_mcp_server.root_checkout_guard.resolve_remote_master_sha", return_value="a" * 40)
-    def test_create_issue_stable_checkout_rejected(self, _git, _get_all, mock_api, _role, _ns, _prof, _auth):
+    @patch(
+        "gitea_mcp_server.issue_lock_worktree.read_worktree_git_state",
+        return_value={
+            "current_branch": "master",
+            "head_sha": "a" * 40,
+            "porcelain_status": "",
+        },
+    )
+    def test_create_issue_stable_checkout_rejected(
+        self, _git, _remote_sha, _get_all, mock_api, _role, _ns, _prof, _auth,
+    ):
         # Without worktree_path/env hints, workspace resolves to PROJECT_ROOT. When that
         # path is the stable control checkout (not under branches/), mutation must fail.
         with patch.object(srv, "PROJECT_ROOT", CONTROL_CHECKOUT_ROOT):

tests/test_root_checkout_guard.py

@@ -0,0 +1,161 @@
+"""Tests for root checkout guard (#475)."""
+
+from __future__ import annotations
+
+import os
+import sys
+import unittest
+from pathlib import Path
+from unittest.mock import patch
+
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent))
+
+import gitea_mcp_server as srv  # noqa: E402
+import root_checkout_guard as rcg  # noqa: E402
+
+CONTROL_ROOT = str(Path(__file__).resolve().parents[3])
+BRANCHES_WORKTREE = str(Path(__file__).resolve().parents[1])
+MASTER_SHA = "a" * 40
+OTHER_SHA = "b" * 40
+
+
+class TestAssessRootCheckoutGuard(unittest.TestCase):
+    def _assess(self, **kwargs):
+        defaults = {
+            "workspace_path": CONTROL_ROOT,
+            "canonical_repo_root": CONTROL_ROOT,
+            "current_branch": "master",
+            "head_sha": MASTER_SHA,
+            "porcelain_status": "",
+            "remote_master_sha": MASTER_SHA,
+            "resolved_role": "author",
+        }
+        defaults.update(kwargs)
+        return rcg.assess_root_checkout_guard(**defaults)
+
+    def test_clean_master_control_checkout_allowed(self):
+        result = self._assess()
+        self.assertTrue(result["proven"])
+        self.assertFalse(result["block"])
+
+    def test_branches_worktree_allowed_for_author(self):
+        result = self._assess(
+            workspace_path=BRANCHES_WORKTREE,
+            current_branch="feat/issue-475-root-checkout-guard",
+            head_sha=OTHER_SHA,
+            resolved_role="author",
+        )
+        self.assertTrue(result["proven"])
+
+    def test_branches_worktree_allowed_for_reviewer(self):
+        result = self._assess(
+            workspace_path=f"{CONTROL_ROOT}/branches/review-pr-1",
+            current_branch="review-pr-1",
+            resolved_role="reviewer",
+        )
+        self.assertTrue(result["proven"])
+
+    def test_reconciler_always_allowed(self):
+        result = self._assess(
+            current_branch="feat/some-branch",
+            head_sha=OTHER_SHA,
+            porcelain_status=" M gitea_mcp_server.py\n",
+            resolved_role="reconciler",
+        )
+        self.assertTrue(result["proven"])
+
+    def test_feature_branch_on_control_checkout_blocked(self):
+        result = self._assess(
+            current_branch="feat/issue-99-example",
+            head_sha=OTHER_SHA,
+        )
+        self.assertTrue(result["block"])
+        self.assertIn("not a stable base branch", result["reasons"][0])
+
+    def test_detached_head_blocked(self):
+        result = self._assess(current_branch=None)
+        self.assertTrue(result["block"])
+        self.assertIn("detached HEAD", result["reasons"][0])
+
+    def test_dirty_control_checkout_blocked(self):
+        result = self._assess(porcelain_status=" M gitea_mcp_server.py\n")
+        self.assertTrue(result["block"])
+        self.assertIn("tracked local edits", result["reasons"][0])
+
+    def test_head_behind_prgs_master_blocked(self):
+        result = self._assess(
+            head_sha=OTHER_SHA,
+            remote_master_sha=MASTER_SHA,
+        )
+        self.assertTrue(result["block"])
+        self.assertIn("does not match prgs/master", result["reasons"][0])
+
+    def test_merger_requires_clean_control_checkout(self):
+        result = self._assess(
+            workspace_path=BRANCHES_WORKTREE,
+            current_branch="feat/issue-475-root-checkout-guard",
+            head_sha=OTHER_SHA,
+            resolved_role="merger",
+        )
+        self.assertTrue(result["block"])
+
+
+class TestVerifyPreflightRootGuardIntegration(unittest.TestCase):
+    def setUp(self):
+        srv._preflight_whoami_called = True
+        srv._preflight_capability_called = True
+        srv._preflight_resolved_role = "reviewer"
+        srv._preflight_whoami_violation = False
+        srv._preflight_capability_violation = False
+        self._orig_in_test = srv._preflight_in_test_mode
+        srv._preflight_in_test_mode = lambda: False
+
+    def tearDown(self):
+        srv._preflight_in_test_mode = self._orig_in_test
+
+    @patch("gitea_mcp_server._get_workspace_porcelain", return_value="")
+    @patch("gitea_mcp_server.root_checkout_guard.resolve_remote_master_sha", return_value=MASTER_SHA)
+    @patch("gitea_mcp_server.issue_lock_worktree.read_worktree_git_state")
+    @patch("gitea_mcp_server._resolve_author_mutation_context")
+    def test_reviewer_from_contaminated_root_blocked(
+        self, mock_ctx, mock_git, _remote_sha, _porcelain,
+    ):
+        srv._preflight_capability_baseline_porcelain = ""
+        mock_ctx.return_value = {
+            "workspace_path": CONTROL_ROOT,
+            "canonical_repo_root": CONTROL_ROOT,
+            "process_project_root": CONTROL_ROOT,
+        }
+        mock_git.return_value = {
+            "current_branch": "feat/hijacked-root",
+            "head_sha": OTHER_SHA,
+            "porcelain_status": "",
+        }
+        with self.assertRaises(RuntimeError) as ctx:
+            srv.verify_preflight_purity("prgs", worktree_path=CONTROL_ROOT)
+        self.assertIn("Root checkout guard (#475)", str(ctx.exception))
+        self.assertIn(rcg.REMEDIATION, str(ctx.exception))
+
+    @patch("gitea_mcp_server._get_workspace_porcelain", return_value="")
+    @patch("gitea_mcp_server.root_checkout_guard.resolve_remote_master_sha", return_value=MASTER_SHA)
+    @patch("gitea_mcp_server.issue_lock_worktree.read_worktree_git_state")
+    @patch("gitea_mcp_server._resolve_author_mutation_context")
+    def test_reviewer_from_branches_worktree_allowed(
+        self, mock_ctx, mock_git, _remote_sha, _porcelain,
+    ):
+        srv._preflight_capability_baseline_porcelain = ""
+        mock_ctx.return_value = {
+            "workspace_path": BRANCHES_WORKTREE,
+            "canonical_repo_root": CONTROL_ROOT,
+            "process_project_root": BRANCHES_WORKTREE,
+        }
+        mock_git.return_value = {
+            "current_branch": "feat/issue-475-root-checkout-guard",
+            "head_sha": OTHER_SHA,
+            "porcelain_status": "",
+        }
+        srv.verify_preflight_purity("prgs", worktree_path=BRANCHES_WORKTREE)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_workspace_guard_alignment.py

@@ -126,17 +126,37 @@ class TestRuntimeContextGuardAlignment(unittest.TestCase):
             with mock.patch.dict("os.environ", {"GITEA_TEST_PORCELAIN": ""}, clear=False):
                 srv.verify_preflight_purity(worktree_path=BRANCHES_WORKTREE)
 
-    def test_stable_checkout_still_rejected(self):
+    @mock.patch("gitea_mcp_server.root_checkout_guard.resolve_remote_master_sha", return_value="a" * 40)
+    @mock.patch(
+        "gitea_mcp_server.issue_lock_worktree.read_worktree_git_state",
+        return_value={
+            "current_branch": "master",
+            "head_sha": "a" * 40,
+            "porcelain_status": "",
+        },
+    )
+    def test_stable_checkout_still_rejected(self, _git, _remote_sha):
         with mock.patch.object(srv, "PROJECT_ROOT", CONTROL_ROOT):
             with mock.patch.dict("os.environ", {"GITEA_TEST_PORCELAIN": ""}, clear=False):
                 with self.assertRaises(RuntimeError) as ctx:
                     srv.verify_preflight_purity()
         self.assertIn("stable control checkout", str(ctx.exception))
 
+    @mock.patch("gitea_mcp_server.root_checkout_guard.resolve_remote_master_sha", return_value="a" * 40)
+    @mock.patch(
+        "gitea_mcp_server.issue_lock_worktree.read_worktree_git_state",
+        return_value={
+            "current_branch": "master",
+            "head_sha": "a" * 40,
+            "porcelain_status": "",
+        },
+    )
     @mock.patch("os.path.isdir", return_value=True)
     @mock.patch("os.path.exists", return_value=True)
     @mock.patch("subprocess.run")
-    def test_non_branches_worktree_rejected(self, mock_run, *_exists):
+    def test_non_branches_worktree_rejected(
+        self, mock_run, mock_exists, mock_isdir, _git, _remote_sha,
+    ):
         outside = "/tmp/outside-repo-checkout"
         mock_run.return_value = MagicMock(
             returncode=0,