fix(id_order): keep an orphaned marker blocking while its herdr session is alive (Issue #63)

A create/resume killed after spawning its pane but before registering its
row left a marker whose owner pid was dead; the next same-cwd waiter pruned
it on the pid alone and could start a second session that discovers the
same workspace conversation id (PR #69 review P1).

- Markers record the herdr server. A dead owner's marker is pruned only once
  its row is registered for the attempt (running, newer epoch: the row
  decides) or `_herdr has-session` reports the session gone; an unanswered
  probe counts as alive. On timeout the kill-session command is printed.
- A live marker of another process for the waiter's own session name is kept
  and blocks instead of being deleted; the waiter's own pid's markers go.
- Tests: orphan / registered / gone / same-session / missing pane pid cases,
  and a create-level reproduction against mock herdr (fails before the fix).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

.agents/skills/lib_py/agents/id_order.py

@@ -4,7 +4,9 @@ While a post-discovered agent (agy, codex, hermes, opencode) in a workspace is
  still being created (marker held by a live create/resume process) or is running
 without a recorded conversation id (live pane pid), a second create or resume of
 the same agent type in that workspace waits until the first records its id, up
-to MAM_ID_ORDER_WAIT_S (default 600 s; 0 = do not wait).
+to MAM_ID_ORDER_WAIT_S (default 600 s; 0 = do not wait). A marker whose owner
+died before the row was registered keeps blocking while its herdr session is
+alive (the pane may still discover the workspace id).
 """
 from __future__ import annotations
 
@@ -13,6 +15,7 @@ import fcntl
 import hashlib
 import json
 import os
+import subprocess
 import sys
 import tempfile
 import time
@@ -50,6 +53,24 @@ def pid_alive(pid: int) -> bool:
         return False
 
 
+def herdr_session_alive(server: str, session: str) -> bool:
+    """lib.sh `_herdr has-session` on the marker's herdr server; an unanswered
+    probe counts as alive (the wait stays bounded by MAM_ID_ORDER_WAIT_S)."""
+    skills_dir = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+    env = dict(os.environ)
+    if server:
+        env["HERDR_SESSION_NAME"] = server
+    script = 'source "$1" && _herdr has-session -t "$2"'
+    try:
+        return subprocess.run(
+            ["bash", "-c", script, "_", os.path.join(skills_dir, "lib.sh"), session],
+            env=env, stdin=subprocess.DEVNULL, stdout=subprocess.DEVNULL,
+            stderr=subprocess.DEVNULL, timeout=30,
+        ).returncode == 0
+    except (OSError, subprocess.SubprocessError):
+        return True
+
+
 def order_dir(cwd: str, agent: str, env: Mapping[str, str] = os.environ,
               home: Optional[str] = None) -> str:
     h = home or env.get("HOME") or env.get("HOME_DIR") or os.path.expanduser("~")
@@ -98,7 +119,7 @@ def blockers(state: Dict[str, Any], cwd: str, agent: str, me: str,
         if not isinstance(m, dict):
             continue
         m_sess = str(m.get("session") or "")
-        if not m_sess or m_sess == me or m_sess in found:
+        if not m_sess or m_sess in found:
             continue
         m_cwd = str(m.get("cwd") or "")
         if m_cwd and canonical_cwd(m_cwd) != target_cwd:
@@ -106,9 +127,6 @@ def blockers(state: Dict[str, Any], cwd: str, agent: str, me: str,
         m_agent = str(m.get("agent") or "")
         if m_agent and m_agent != agent:
             continue
-        owner_pid = _parse_pos_int(m.get("owner_pid"))
-        if owner_pid is None or not is_alive(owner_pid):
-            continue
         row = rows_by_name.get(m_sess)
         if row is None:
             found.append(m_sess)
@@ -141,8 +159,24 @@ def blockers(state: Dict[str, Any], cwd: str, agent: str, me: str,
     return found
 
 
-def _read_and_prune_markers(dpath: str, me: str,
-                            is_alive: Callable[[int], bool] = pid_alive) -> List[Dict[str, Any]]:
+def _registered_for_attempt(m: Dict[str, Any], row: Optional[Dict[str, Any]]) -> bool:
+    if not isinstance(row, dict) or row.get("status") != "running":
+        return False
+    return int(row.get("herdr_session_epoch") or 0) > int(m.get("prev_epoch") or 0)
+
+
+def _read_and_prune_markers(dpath: str, me: str, my_pid: int, state: Dict[str, Any],
+                            is_alive: Callable[[int], bool] = pid_alive,
+                            pane_alive: Callable[[str, str], bool] = herdr_session_alive,
+                            ) -> List[Dict[str, Any]]:
+    """Markers that still count. A live owner keeps its marker (another live
+    attempt on `me` included). A dead owner's marker goes once its row is
+    registered for the attempt (the row decides from then on) or its herdr
+    session is gone; until then it is kept as an orphan."""
+    rows_by_name = {
+        str(s.get("name") or ""): s
+        for s in (state.get("herdr_sessions") or []) if isinstance(s, dict)
+    }
     out: List[Dict[str, Any]] = []
     try:
         names = sorted(os.listdir(dpath))
@@ -165,7 +199,18 @@ def _read_and_prune_markers(dpath: str, me: str,
             continue
         owner_pid = _parse_pos_int(data.get("owner_pid"))
         sess = str(data.get("session") or "")
-        if sess == me or owner_pid is None or not is_alive(owner_pid):
+        if owner_pid is None or owner_pid == my_pid:
+            drop = True
+        elif is_alive(owner_pid):
+            drop = False
+        elif sess == me or not sess:
+            drop = True
+        elif _registered_for_attempt(data, rows_by_name.get(sess)):
+            drop = True
+        else:
+            drop = not pane_alive(str(data.get("herdr_server") or ""), sess)
+            data["_orphan"] = True
+        if drop:
             try:
                 os.remove(fpath)
             except OSError:
@@ -176,7 +221,7 @@ def _read_and_prune_markers(dpath: str, me: str,
 
 
 def write_marker(dpath: str, session: str, owner_pid: int, cwd: str, agent: str,
-                 prev_row: Optional[Dict[str, Any]] = None) -> str:
+                 prev_row: Optional[Dict[str, Any]] = None, herdr_server: str = "") -> str:
     os.makedirs(dpath, exist_ok=True)
     marker_path = os.path.join(dpath, f"{session}.json")
     payload: Dict[str, Any] = {
@@ -184,6 +229,7 @@ def write_marker(dpath: str, session: str, owner_pid: int, cwd: str, agent: str,
         "owner_pid": int(owner_pid),
         "cwd": canonical_cwd(cwd),
         "agent": agent,
+        "herdr_server": herdr_server,
         "at": int(time.time()),
     }
     if isinstance(prev_row, dict):
@@ -203,7 +249,9 @@ def wait(cwd: str, agent: str, session: str, owner_pid: int,
          uuid: str = "", yaml_path: Optional[str] = None,
          home: Optional[str] = None, wait_s_val: Optional[int] = None,
          poll: float = 0.25,
-         is_alive: Callable[[int], bool] = pid_alive) -> int:
+         is_alive: Callable[[int], bool] = pid_alive,
+         herdr_server: str = "",
+         pane_alive: Optional[Callable[[str, str], bool]] = None) -> int:
     adapter = get_adapter(agent)
     if adapter is None or adapter.id_lifecycle != POST_DISCOVERED:
         return 0
@@ -215,6 +263,7 @@ def wait(cwd: str, agent: str, session: str, owner_pid: int,
     deadline = time.monotonic() + cap
     announced = False
     row_ref = {"name": session}
+    probe = pane_alive or herdr_session_alive
 
     while True:
         with open(lock_file, "a", encoding="utf-8") as lf:
@@ -230,7 +279,8 @@ def wait(cwd: str, agent: str, session: str, owner_pid: int,
                         file=sys.stderr, flush=True,
                     )
                     return 1
-            markers = _read_and_prune_markers(dpath, session, is_alive=is_alive)
+            markers = _read_and_prune_markers(dpath, session, owner_pid, state,
+                                              is_alive=is_alive, pane_alive=probe)
             blks = blockers(state, cwd, agent, session, markers, is_alive=is_alive)
             if not blks:
                 prev_row = next(
@@ -242,7 +292,8 @@ def wait(cwd: str, agent: str, session: str, owner_pid: int,
                 )
                 already_recorded = bool(uuid) and own_id(prev_row, agent) == uuid
                 if not already_recorded and owner_pid and owner_pid > 0:
-                    write_marker(dpath, session, owner_pid, cwd, agent, prev_row=prev_row)
+                    write_marker(dpath, session, owner_pid, cwd, agent, prev_row=prev_row,
+                                 herdr_server=herdr_server)
                 return 0
 
         names = ", ".join(blks)
@@ -253,6 +304,15 @@ def wait(cwd: str, agent: str, session: str, owner_pid: int,
                 f"or stop it with multi-agent-mux-stop.",
                 file=sys.stderr, flush=True,
             )
+            for m in markers:
+                if m.get("_orphan") and m.get("session") in blks:
+                    srv = m.get("herdr_server") or "default"
+                    print(
+                        f"ERROR: {m['session']}'s create/resume exited before recording it, "
+                        f"but its herdr session is alive; close it with: "
+                        f"HERDR_SESSION_NAME={srv} herdr kill-session -t {m['session']}",
+                        file=sys.stderr, flush=True,
+                    )
             return 1
         if not announced:
             print(
@@ -275,6 +335,7 @@ def main(argv: Optional[List[str]] = None) -> int:
     s_wait.add_argument("--session", required=True)
     s_wait.add_argument("--owner-pid", type=int, default=0)
     s_wait.add_argument("--uuid", default="")
+    s_wait.add_argument("--herdr-server", default="")
     a = p.parse_args(argv)
     return wait(
         cwd=a.cwd,
@@ -282,6 +343,7 @@ def main(argv: Optional[List[str]] = None) -> int:
         session=a.session,
         owner_pid=a.owner_pid,
         uuid=a.uuid or "",
+        herdr_server=a.herdr_server or "",
     )