fix: document + tool the macOS com.apple.provenance workaround (#3)

Root cause: macOS Sequoia+ blocks Python.app from executing files carrying the
com.apple.provenance extended attribute. Files written by an agent/IDE terminal
get it (shell scripts and pre-session files do not). This is a macOS security
feature, not a bug in our code — so the fix is an operator workaround, not a
code change to the tools.

- scripts/clear-provenance: recursively removes ONLY com.apple.provenance under
  a path (default: repo root); tolerates files without it; leaves other xattrs
  intact; supports --dry-run. Advises running from a Full-Disk-Access terminal.
- README Troubleshooting section documenting the symptom, the helper, manual
  xattr equivalents, and the Full Disk Access alternative.

Narrow + macOS-specific; no auth/release/worktree/tracker/MCP behavior changed.

Tests: tests/test_clear_provenance.py (6 cases) — dry-run default/explicit path,
missing-path error, bad-flag/too-many-args exit 2, and that only
com.apple.provenance is targeted (not a blanket xattr clear). Dry-run only; no
real xattr mutation.

bash -n clean; py_compile mcp_server.py clean; full suite 319 passed / 0
failures; git diff --check clean; no secrets.

Closes #3.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

README.md

@@ -382,3 +382,35 @@ python3 -m pytest tests/ -v
 | `test_mirror_refs.py`   | Flags, safety defaults, local integration tests |
 
 All tests mock network and keychain access — no real API calls are made.
+
+## Troubleshooting
+
+### macOS: `com.apple.provenance` blocks Python execution (#3)
+
+On macOS Sequoia and later, files written by an agent/IDE terminal receive the
+`com.apple.provenance` extended attribute, and macOS blocks `Python.app` from
+**executing** such files. Symptoms: newly created/restored `.py` files fail to
+run (e.g. `create_issue.py` "vanishing" or refusing to execute), while shell
+scripts and files created before the session are unaffected. This is a macOS
+security feature, not a bug in this project's code.
+
+Workarounds (run from a terminal with **Full Disk Access**, e.g. `Terminal.app`
+— not the IDE terminal, or the removal itself may be blocked):
+
+```bash
+# Preferred: strip only com.apple.provenance under the repo (dry-run first)
+./scripts/clear-provenance --dry-run
+./scripts/clear-provenance
+
+# Or a single file
+./scripts/clear-provenance /path/to/file.py
+
+# Manual equivalents
+xattr -r -d com.apple.provenance /Users/jasonwalker/Development/Gitea-Tools/
+xattr -cr /Users/jasonwalker/Development/Gitea-Tools/   # clears ALL xattrs
+```
+
+Alternatively, grant Full Disk Access to the terminal app in
+**System Settings → Privacy & Security**. `scripts/clear-provenance` removes only
+`com.apple.provenance` (leaving other extended attributes intact) and supports
+`--dry-run`.

scripts/clear-provenance

@@ -0,0 +1,61 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# clear-provenance — strip the macOS com.apple.provenance extended attribute so
+# Python.app can execute .py files created by agent/IDE terminals (issue #3).
+#
+# macOS Sequoia+ blocks Python.app from executing files carrying
+# com.apple.provenance. Files written by the agent terminal get it; shell
+# scripts are unaffected. This is a macOS security feature, not a bug in our
+# code — see the Troubleshooting section of the README.
+#
+# Run from a terminal with Full Disk Access (e.g. Terminal.app), not the IDE
+# terminal, or the removal itself may be blocked.
+
+usage() {
+  cat <<'EOF'
+usage: scripts/clear-provenance [--dry-run] [path]
+
+Recursively remove the com.apple.provenance extended attribute under <path>
+(default: the repository root). macOS only. Only that attribute is removed;
+other extended attributes are left intact.
+
+Examples:
+  scripts/clear-provenance --dry-run
+  scripts/clear-provenance
+  scripts/clear-provenance /path/to/file.py
+EOF
+}
+
+dry_run=0
+while [[ "${1:-}" == --* ]]; do
+  case "$1" in
+    --dry-run) dry_run=1 ;;
+    --help) usage; exit 0 ;;
+    *) usage >&2; exit 2 ;;
+  esac
+  shift
+done
+
+if [[ $# -gt 1 ]]; then
+  usage >&2
+  exit 2
+fi
+
+script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+repo_root="$(cd "$script_dir/.." && pwd)"
+target="${1:-$repo_root}"
+
+if [[ ! -e "$target" ]]; then
+  printf 'clear-provenance: no such path: %s\n' "$target" >&2
+  exit 1
+fi
+
+# Remove only com.apple.provenance; tolerate files that do not carry it.
+if [[ "$dry_run" -eq 1 ]]; then
+  printf 'clear-provenance: [dry-run] would run: xattr -r -d com.apple.provenance %q\n' "$target"
+  exit 0
+fi
+
+xattr -r -d com.apple.provenance "$target" 2>/dev/null || true
+printf 'clear-provenance: removed com.apple.provenance recursively under: %s\n' "$target"

tests/test_clear_provenance.py

@@ -0,0 +1,60 @@
+"""Tests for scripts/clear-provenance (#3).
+
+Exercises argument handling and the inert --dry-run path only — no real xattr
+mutation, no network. (Actually removing com.apple.provenance is macOS-only and
+has real side effects, so it is not exercised here.)
+"""
+import subprocess
+import tempfile
+import unittest
+from pathlib import Path
+
+REPO = Path(__file__).resolve().parent.parent
+SCRIPT = REPO / "scripts" / "clear-provenance"
+
+
+def run(*args):
+    proc = subprocess.run(["bash", str(SCRIPT), *args],
+                          capture_output=True, text=True, cwd=str(REPO))
+    return proc.returncode, proc.stdout, proc.stderr
+
+
+class TestClearProvenance(unittest.TestCase):
+
+    def test_dry_run_defaults_to_repo_root(self):
+        rc, out, _ = run("--dry-run")
+        self.assertEqual(rc, 0)
+        self.assertIn("would run: xattr -r -d com.apple.provenance", out)
+        self.assertIn(str(REPO), out)
+
+    def test_dry_run_explicit_path(self):
+        with tempfile.TemporaryDirectory() as d:
+            f = Path(d) / "x.py"
+            f.write_text("print('hi')\n")
+            rc, out, _ = run("--dry-run", str(f))
+            self.assertEqual(rc, 0)
+            self.assertIn(str(f), out)
+
+    def test_missing_path_errors(self):
+        rc, _, err = run("--dry-run", "/no/such/path-xyz")
+        self.assertEqual(rc, 1)
+        self.assertIn("no such path", err)
+
+    def test_bad_flag_exit_2(self):
+        rc, _, _ = run("--bogus")
+        self.assertEqual(rc, 2)
+
+    def test_too_many_args_exit_2(self):
+        rc, _, _ = run("a", "b")
+        self.assertEqual(rc, 2)
+
+    def test_only_targets_provenance_attribute(self):
+        # The command removes only com.apple.provenance, not all xattrs.
+        rc, out, _ = run("--dry-run")
+        self.assertIn("com.apple.provenance", out)
+        self.assertNotIn("xattr -rc", out)   # not a blanket "clear all"
+        self.assertNotIn("-c ", out)
+
+
+if __name__ == "__main__":
+    unittest.main()