Keep Pulse on explicit Stampede roots

When AGENT_PULSE_SCAN_ROOTS is set, restrict Stampede run discovery to those roots and sort run directories by run id timestamp before mtime so terminal Agent Conductor runs do not fall back to stale historical runs.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: Gregg Cochran

agent_pulse.py

@@ -1010,18 +1010,19 @@ def _iter_stampede_bases(self) -> List[Path]:
             for p in os.environ.get("AGENT_PULSE_SCAN_ROOTS", "").split(os.pathsep)
             if p
         ]
-        roots = [Path.cwd(), Path.home(), Path.home() / "dev", Path.home() / "tmp", *env_roots]
+        roots = env_roots if env_roots else [Path.cwd(), Path.home(), Path.home() / "dev", Path.home() / "tmp"]
         bases: Dict[str, Path] = {}
 
         def add_base(path: Path) -> None:
-            if path.exists() and path.is_dir():
+            if path.exists() and path.is_dir() and path.name == ".stampede":
                 bases[str(path)] = path
 
         def scan_depth(root: Path, max_depth: int = 3) -> None:
             stack: List[Tuple[Path, int]] = [(root, 0)]
             while stack and len(bases) < 100:
                 current, depth = stack.pop()
                 try:
+                    add_base(current)
                     add_base(current / ".stampede")
                     if depth >= max_depth:
                         continue
@@ -1065,13 +1066,20 @@ def _candidate_run_dirs(self) -> List[Path]:
             except Exception:
                 continue
 
-        def mtime(path: Path) -> float:
+        def run_sort_key(path: Path) -> Tuple[int, float]:
+            match = re.match(r"run-(\d{8})-(\d{6})$", path.name)
+            run_ts = 0
+            if match:
+                try:
+                    run_ts = int(datetime.strptime("".join(match.groups()), "%Y%m%d%H%M%S").timestamp())
+                except Exception:
+                    run_ts = 0
             try:
-                return path.stat().st_mtime
+                return (run_ts, path.stat().st_mtime)
             except OSError:
-                return 0.0
+                return (run_ts, 0.0)
 
-        return sorted(runs.values(), key=mtime, reverse=True)[: self._RUN_DIR_LIMIT]
+        return sorted(runs.values(), key=run_sort_key, reverse=True)[: self._RUN_DIR_LIMIT]
 
     def _poll_ledger_events(self, ledger: Path, run_id: str, commander_id: str) -> None:
         key = f"stampede-ledger:{ledger}"