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

.agents/skills/lib_py/agents/base.py

@@ -1,10 +1,53 @@
 # base.py — BaseAgentAdapter abstract base class, SpawnSpec, and DiscoveryContext
 
-import os, json, sqlite3
+import os, json, sqlite3, shutil, subprocess
 from typing import Optional, Dict, Any, List
 from lib_py.paths import resolve_home
 from lib_py.verify_session import verify_session_uuid, workspace_key
 
+
+def conversation_in_use(uuid: str, paths=()) -> bool:
+    """A live process still references the conversation (Issues #10, #13).
+
+    Either its id is on a command line other than this process's own lineage
+    (`claude -r <uuid>`, `agy --conversation <uuid>`, ... - the purge command
+    itself names the uuid, so its ancestors are excluded), or one of `paths`
+    is held open (lsof, where available). A purge must not touch a
+    conversation that is in use.
+    """
+    try:
+        out = subprocess.run(["ps", "-axo", "pid=,ppid=,command="],
+                             capture_output=True, text=True, timeout=10).stdout
+    except Exception:
+        out = ""
+    parents: Dict[int, int] = {}
+    holders: List[int] = []
+    for line in out.splitlines():
+        parts = line.split(None, 2)
+        if len(parts) < 2 or not (parts[0].isdigit() and parts[1].isdigit()):
+            continue
+        pid, ppid = int(parts[0]), int(parts[1])
+        parents[pid] = ppid
+        if len(parts) > 2 and uuid in parts[2]:
+            holders.append(pid)
+    if holders:
+        lineage = set()
+        p = os.getpid()
+        while p and p not in lineage:
+            lineage.add(p)
+            p = parents.get(p, 0)
+        if any(h not in lineage for h in holders):
+            return True
+    existing = [p for p in paths if p and os.path.exists(p)]
+    if existing and shutil.which("lsof"):
+        try:
+            r = subprocess.run(["lsof", "-t"] + existing, capture_output=True, text=True, timeout=10)
+            if r.stdout.strip():
+                return True
+        except Exception:
+            pass
+    return False
+
 class SpawnSpec:
     def __init__(self, agent_name: str, session_name: str, command: str, env: Optional[Dict[str, str]] = None):
         self.agent_name = agent_name
@@ -107,6 +150,15 @@ class BaseAgentAdapter:
     def purge_artifacts(self, uuid: str, ctx: DiscoveryContext) -> list:
         raise NotImplementedError
 
+    def residual_artifacts(self, uuid: str, ctx: DiscoveryContext) -> list:
+        """Paths still carrying `uuid` after a purge. Adapters that know their
+        on-disk tree override this; the default has nothing to scan."""
+        return []
+
+    def conversation_in_use(self, uuid: str, ctx: DiscoveryContext) -> bool:
+        """True while a live process still references the conversation."""
+        return conversation_in_use(uuid, [self.artifact_path(uuid, ctx)])
+
     def spawn_spec(self, binary: str, session_uuid: str = "", use_wrapper: bool = False) -> str:
         raise NotImplementedError