fix(issue-10,11,13,15): complete agy purge, orchestrator purge, workspace-anchored registry

Issue #10 - agy purge_artifacts left resumable pieces behind: it now also
removes the SQLite sidecars (-wal/-shm/-journal), the title annotation and
the presence lock (the lock only once no live process references the
conversation), and residual_artifacts() reports anything under
~/.gemini/antigravity-cli still carrying the uuid.

Issue #13 - the orchestrator has no herdr_sessions row, so its conversation
could not be purged by any skill. `lib_py.agents purge <agent|auto> <uuid>`
resolves the adapter from what is on disk (orchestrator_uuids stores bare
uuids), refuses while a live process names the uuid (conversation_in_use:
process list minus the caller's own lineage, plus lsof), and prints what it
purged. `orc_onboard.sh --remove <uuid> --purge-conversation --yes [--agent]`
runs it before the registry update so a refusal changes nothing (exit 4
without --yes, 5 while in use).

Issue #11 - "Successfully removeed": conjugate add/remove explicitly.

Issue #15 - the job registry and audit log followed the caller's cwd, so the
pytest suite (create_session.sh with its default onboarding job, run from the
repo root) had left 593 test records in the real .mam/jobs. Defaults now
resolve MAM_JOBS_DIR / DELEGATE_JOB_LOGS_DIR, then $WORKSPACE_ROOT/.mam/...,
then the cwd (mqtt_common.default_registry_dir / get_logs_dir; registry.py,
publish_event.py, service.py, create_session.sh, stop_session.sh); the
sandbox fixture pins both. The tier suites that used to leak now leave the
real registry untouched (881 records before and after).

Tests: test_issue10_13_purge.py (13), test_issue15_registry_isolation.py (7);
T-O13 pins the corrected message; the R1 helper test and B-9 logs-dir test
now assert the workspace-anchored contract; publish_event snapshot updated.

Refs #10 #11 #13 #15

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01VCgu9Fa9iT7TbJUSzdq4Ff

tests/test_issue10_13_purge.py

@@ -0,0 +1,264 @@
+#!/usr/bin/env python3
+"""Issues #10 and #13 — purging a conversation must leave nothing resumable
+behind, and an orchestrator conversation (no herdr_sessions row) must be
+purgeable through orc_onboard.sh.
+
+#10: the agy adapter deleted only the conversation DB and the brain dir; the
+     SQLite sidecars (-wal/-shm/-journal), the title annotation and the presence
+     lock survived. The lock is removed only once nothing references the
+     conversation any more.
+#13: `orc_onboard.sh --remove <uuid> --purge-conversation --yes` resolves the
+     adapter from what is on disk (orchestrator_uuids stores bare UUIDs), purges
+     through it, and refuses while a live process still names the UUID.
+"""
+from __future__ import annotations
+
+import json
+import os
+import sqlite3
+import subprocess
+import sys
+import time
+from pathlib import Path
+
+import pytest
+
+REPO_ROOT = Path(__file__).resolve().parent.parent
+SKILLS = REPO_ROOT / ".agents" / "skills"
+ONBOARD_SH = SKILLS / "multi-agent-mux-orc-onboard" / "scripts" / "orc_onboard.sh"
+
+sys.path.insert(0, str(SKILLS))
+from lib_py.agents.registry import get_adapter  # noqa: E402
+from lib_py.agents.base import DiscoveryContext, conversation_in_use  # noqa: E402
+
+UUID = "7d0b6f12-3a4c-4e5f-8a9b-0c1d2e3f4a5b"
+OTHER = "11111111-2222-4333-8444-555555555555"
+
+
+def _agy_tree(home: Path, uuid: str) -> dict:
+    root = home / ".gemini" / "antigravity-cli"
+    paths = {
+        "db": root / "conversations" / f"{uuid}.db",
+        "wal": root / "conversations" / f"{uuid}.db-wal",
+        "shm": root / "conversations" / f"{uuid}.db-shm",
+        "brain": root / "brain" / uuid,
+        "annotation": root / "annotations" / f"{uuid}.pbtxt",
+        "lock": root / "presence" / f"{uuid}.lock",
+    }
+    for key, p in paths.items():
+        if key == "brain":
+            p.mkdir(parents=True, exist_ok=True)
+            (p / "note.txt").write_text("brain")
+        elif key == "db":
+            # A real conversation DB: the adapter's verify_artifact opens it
+            # with sqlite3, and sqlite discards a garbage -wal next to a
+            # garbage main file, which would hide the sidecar from the purge.
+            p.parent.mkdir(parents=True, exist_ok=True)
+            conn = sqlite3.connect(p)
+            conn.execute("CREATE TABLE steps (id INTEGER)")
+            conn.execute("INSERT INTO steps VALUES (1)")
+            conn.commit()
+            conn.close()
+        else:
+            p.parent.mkdir(parents=True, exist_ok=True)
+            p.write_text("x" if key != "lock" else "")
+    return paths
+
+
+def _holder(uuid: str) -> subprocess.Popen:
+    """A live process whose command line names the conversation, the way a
+    resumed `agy --conversation <uuid>` or `claude -r <uuid>` does. (Not
+    `sh -c 'sleep …'`: a shell execs its last simple command and the uuid
+    would vanish from the process list.)"""
+    proc = subprocess.Popen([sys.executable, "-c", "import sys, time; time.sleep(60)", "--conversation", uuid])
+    time.sleep(0.3)
+    return proc
+
+
+def _stop(proc: subprocess.Popen) -> None:
+    proc.kill()
+    proc.wait(timeout=10)
+
+
+def _run_onboard(args, sandbox: Path, extra_env=None) -> subprocess.CompletedProcess:
+    env = dict(os.environ)
+    for k in ("CLAUDE_CODE_SESSION_ID", "ANTIGRAVITY_CONVERSATION_ID", "HERMES_SESSION_ID", "MAM_ORCHESTRATOR_UUIDS"):
+        env.pop(k, None)
+    env.update({
+        "PYTHONPATH": f"{SKILLS}:{env.get('PYTHONPATH', '')}",
+        "AGENT_SESSIONS_YAML": str(sandbox / ".mam" / "agent-sessions.yaml"),
+        "YAML_PATH": str(sandbox / ".mam" / "agent-sessions.yaml"),
+        "HOME_DIR": str(sandbox),
+        "AGENT_PYTHON_BIN": sys.executable,
+        "DELEGATE_JOB_PYTHON": sys.executable,
+    })
+    if extra_env:
+        env.update(extra_env)
+    return subprocess.run(["bash", str(ONBOARD_SH)] + list(args), capture_output=True, text=True,
+                          env=env, cwd=str(sandbox), timeout=120)
+
+
+def _registered(sandbox: Path, uuid: str) -> bool:
+    return uuid in _run_onboard(["--list"], sandbox).stdout
+
+
+# ---------------------------------------------------------------------------
+# #10 — agy adapter
+# ---------------------------------------------------------------------------
+def test_agy_purge_removes_sidecars_annotation_and_lock(tmp_path):
+    paths = _agy_tree(tmp_path, UUID)
+    adapter = get_adapter("agy")
+    ctx = DiscoveryContext(workspace=str(tmp_path), agent_name="agy", home_dir=str(tmp_path))
+
+    purged = adapter.purge_artifacts(UUID, ctx)
+
+    assert len(purged) == 6, purged
+    for key, p in paths.items():
+        assert not p.exists(), f"{key} survived the purge: {p}"
+    assert adapter.residual_artifacts(UUID, ctx) == []
+
+
+def test_agy_purge_keeps_presence_lock_while_in_use(tmp_path):
+    paths = _agy_tree(tmp_path, UUID)
+    adapter = get_adapter("agy")
+    ctx = DiscoveryContext(workspace=str(tmp_path), agent_name="agy", home_dir=str(tmp_path))
+    holder = _holder(UUID)
+    try:
+        purged = adapter.purge_artifacts(UUID, ctx)
+    finally:
+        _stop(holder)
+
+    assert paths["lock"].exists(), "presence lock must survive while a process references the conversation"
+    assert str(paths["lock"]) not in purged
+    for key in ("db", "wal", "shm", "brain", "annotation"):
+        assert not paths[key].exists(), key
+    assert adapter.residual_artifacts(UUID, ctx) == [str(paths["lock"])]
+
+
+def test_agy_purge_reports_only_what_existed(tmp_path):
+    """The historical 2-item contract (db + brain) still holds when no sidecar
+    exists (test_a4_adapter_contract pins len == 2)."""
+    root = tmp_path / ".gemini" / "antigravity-cli"
+    (root / "conversations").mkdir(parents=True)
+    (root / "conversations" / f"{UUID}.db").write_text("db")
+    (root / "brain" / UUID).mkdir(parents=True)
+    adapter = get_adapter("agy")
+    ctx = DiscoveryContext(workspace=str(tmp_path), agent_name="agy", home_dir=str(tmp_path))
+    assert len(adapter.purge_artifacts(UUID, ctx)) == 2
+
+
+def test_conversation_in_use_ignores_own_lineage():
+    """The purge command names the uuid on its own command line (and its
+    parent shell does); only *other* processes count as holders."""
+    assert conversation_in_use(OTHER) is False
+    holder = _holder(OTHER)
+    try:
+        assert conversation_in_use(OTHER) is True
+    finally:
+        _stop(holder)
+    assert conversation_in_use(OTHER) is False
+
+
+# ---------------------------------------------------------------------------
+# #13 — lib_py.agents purge CLI
+# ---------------------------------------------------------------------------
+def _purge_cli(agent: str, uuid: str, home: Path) -> subprocess.CompletedProcess:
+    env = dict(os.environ, HOME_DIR=str(home), PYTHONPATH=f"{SKILLS}:{os.environ.get('PYTHONPATH', '')}")
+    return subprocess.run([sys.executable, "-m", "lib_py.agents", "purge", agent, uuid, str(home)],
+                          capture_output=True, text=True, env=env, cwd=str(home), timeout=60)
+
+
+def test_purge_cli_auto_resolves_agy_from_disk(tmp_path):
+    paths = _agy_tree(tmp_path, UUID)
+    res = _purge_cli("auto", UUID, tmp_path)
+    assert res.returncode == 0, res.stderr
+    out = json.loads(res.stdout)
+    assert out["agent"] == "agy"
+    assert len(out["purged"]) == 6 and out["residual"] == [] and out["in_use"] is False
+    assert not any(p.exists() for p in paths.values())
+
+
+def test_purge_cli_refuses_while_in_use(tmp_path):
+    paths = _agy_tree(tmp_path, UUID)
+    holder = _holder(UUID)
+    try:
+        res = _purge_cli("agy", UUID, tmp_path)
+    finally:
+        _stop(holder)
+    assert res.returncode == 4, res.stdout + res.stderr
+    assert json.loads(res.stdout)["in_use"] is True
+    assert all(p.exists() for p in paths.values()), "a refused purge must remove nothing"
+
+
+def test_purge_cli_unresolved_uuid(tmp_path):
+    res = _purge_cli("auto", OTHER, tmp_path)
+    assert res.returncode == 5, res.stdout + res.stderr
+    assert json.loads(res.stdout)["agent"] is None
+
+
+# ---------------------------------------------------------------------------
+# #13 — orc_onboard.sh --remove --purge-conversation
+# ---------------------------------------------------------------------------
+def test_orc_remove_purge_requires_yes(mam_sandbox):
+    paths = _agy_tree(mam_sandbox, UUID)
+    assert _run_onboard(["--uuid", UUID], mam_sandbox).returncode == 0
+
+    res = _run_onboard(["--remove", UUID, "--purge-conversation"], mam_sandbox)
+
+    assert res.returncode == 4, res.stdout + res.stderr
+    assert "Re-run with --yes" in res.stderr
+    assert all(p.exists() for p in paths.values())
+    assert _registered(mam_sandbox, UUID), "registration must be untouched without --yes"
+
+
+def test_orc_remove_purge_deletes_and_unregisters(mam_sandbox):
+    paths = _agy_tree(mam_sandbox, UUID)
+    assert _run_onboard(["--uuid", UUID], mam_sandbox).returncode == 0
+
+    res = _run_onboard(["--remove", UUID, "--purge-conversation", "--yes"], mam_sandbox)
+
+    assert res.returncode == 0, res.stdout + res.stderr
+    assert "Successfully removed orchestrator UUID" in res.stdout
+    assert res.stdout.count("purged: ") == 6, res.stdout
+    assert "residual: none (agent: agy)" in res.stdout
+    assert not any(p.exists() for p in paths.values())
+    assert not _registered(mam_sandbox, UUID)
+
+
+def test_orc_remove_purge_refused_while_in_use(mam_sandbox):
+    paths = _agy_tree(mam_sandbox, UUID)
+    assert _run_onboard(["--uuid", UUID], mam_sandbox).returncode == 0
+    holder = _holder(UUID)
+    try:
+        res = _run_onboard(["--remove", UUID, "--purge-conversation", "--yes"], mam_sandbox)
+    finally:
+        _stop(holder)
+
+    assert res.returncode == 5, res.stdout + res.stderr
+    assert "still in use" in res.stderr
+    assert all(p.exists() for p in paths.values())
+    assert _registered(mam_sandbox, UUID), "a refused purge must leave the registration in place"
+
+
+def test_orc_remove_purge_without_artifacts_still_unregisters(mam_sandbox):
+    assert _run_onboard(["--uuid", UUID], mam_sandbox).returncode == 0
+    res = _run_onboard(["--remove", UUID, "--purge-conversation", "--yes"], mam_sandbox)
+    assert res.returncode == 0, res.stdout + res.stderr
+    assert "nothing to purge" in res.stderr
+    assert not _registered(mam_sandbox, UUID)
+
+
+def test_orc_purge_flag_needs_remove(mam_sandbox):
+    res = _run_onboard(["--uuid", UUID, "--purge-conversation", "--yes"], mam_sandbox)
+    assert res.returncode == 2
+    assert not _registered(mam_sandbox, UUID)
+
+
+def test_orc_dry_run_purge_changes_nothing(mam_sandbox):
+    paths = _agy_tree(mam_sandbox, UUID)
+    assert _run_onboard(["--uuid", UUID], mam_sandbox).returncode == 0
+    res = _run_onboard(["--remove", UUID, "--purge-conversation", "--yes", "--dry-run"], mam_sandbox)
+    assert res.returncode == 0
+    assert "purge its conversation artifacts" in res.stdout
+    assert all(p.exists() for p in paths.values())
+    assert _registered(mam_sandbox, UUID)