diff --git a/cli.py b/cli.py
index bc4f4a76befb..b85c8dd65161 100644
--- a/cli.py
+++ b/cli.py
@@ -1165,6 +1165,40 @@ def _reset_terminal_input_modes_on_exit() -> None:
 _active_worktree: Optional[Dict[str, str]] = None
 
 
+def _build_concurrent_sessions_note(concurrent: list) -> str:
+    """Build a structured block for the agent's system prompt.
+
+    When another Hermes session is active in the same git repository the agent
+    must know about it so it avoids destructive operations (reset --hard,
+    rebase, checkout --) that would clobber the other session's in-flight work.
+
+    Returns an empty string when there are no concurrent sessions.
+    """
+    if not concurrent:
+        return ''
+    import datetime as _dt
+    lines = [
+        '[Concurrent sessions]',
+        'Other active Hermes sessions are open in this repository:',
+    ]
+    for e in concurrent:
+        sid = (e.get('session_id') or '?')[:24]
+        pid = e.get('pid', '?')
+        branch = (e.get('metadata') or {}).get('branch', 'unknown')
+        started_raw = e.get('started_at')
+        try:
+            started = _dt.datetime.fromtimestamp(float(started_raw)).strftime('%H:%M:%S')
+        except Exception:
+            started = str(started_raw or '?')
+        lines.append(f'- ID: {sid}, branch: {branch}, PID: {pid}, started: {started}')
+    lines.append(
+        'Uncommitted changes may exist in the shared working tree. '
+        'Avoid destructive git operations (reset --hard, checkout --, rebase) '
+        'unless you have confirmed no other session holds in-flight work.'
+    )
+    return '\n'.join(lines)
+
+
 def _normalize_git_bash_path(p: Optional[str]) -> Optional[str]:
     """Translate a Git Bash-style path (``/c/Users/...``) to the native
     Windows form (``C:\\Users\\...``) that Python's ``subprocess.Popen``
@@ -1340,6 +1374,17 @@ def _setup_worktree(repo_root: str = None) -> Optional[Dict[str, str]]:
         except Exception as e:
             logger.debug("Error copying .worktreeinclude entries: %s", e)
 
+    # Lock the worktree so other processes (and `git worktree remove`) can see
+    # it is actively in use.  Fail-soft: a lock failure never blocks the session.
+    try:
+        subprocess.run(
+            ["git", "worktree", "lock", "--reason", f"hermes pid={os.getpid()}", str(wt_path)],
+            capture_output=True, text=True, timeout=10, cwd=repo_root,
+        )
+        logger.debug("Worktree locked: %s (pid=%s)", wt_path, os.getpid())
+    except Exception as e:
+        logger.debug("git worktree lock failed (non-fatal): %s", e)
+
     info = {
         "path": str(wt_path),
         "branch": branch_name,
@@ -1405,6 +1450,16 @@ def _cleanup_worktree(info: Dict[str, str] = None) -> None:
     if not Path(wt_path).exists():
         return
 
+    # Unlock before removal so `git worktree remove` succeeds even when a
+    # lock was placed at creation time.  Fail-soft — never block cleanup.
+    try:
+        subprocess.run(
+            ["git", "worktree", "unlock", wt_path],
+            capture_output=True, text=True, timeout=10, cwd=repo_root,
+        )
+    except Exception as e:
+        logger.debug("git worktree unlock failed (non-fatal): %s", e)
+
     has_unpushed = _worktree_has_unpushed_commits(wt_path, timeout=10)
 
     if has_unpushed:
@@ -3612,10 +3667,16 @@ def _claim_active_session(self, surface: str = "cli", *, stderr: bool = False) -
         try:
             from hermes_cli.active_sessions import try_acquire_active_session
 
+            # Store repo_root in the registry entry so that
+            # find_concurrent_repo_sessions() can match sessions by repository.
+            _repo_root = getattr(self, '_repo_root', None) or _git_repo_root()
+            _meta = {'repo_root': _repo_root} if _repo_root else None
+
             lease, message = try_acquire_active_session(
                 session_id=self.session_id,
                 surface=surface,
                 config=self.config,
+                metadata=_meta,
             )
         except Exception as exc:
             logger.warning("Failed to claim active session slot: %s", exc)
@@ -10959,6 +11020,27 @@ def run(self):
             pass
 
         self.show_banner()
+        # Warn when another Hermes session is already running in the same repo.
+        # Both sessions share the working tree and can clobber each other's
+        # uncommitted changes.  We also inject a note into system_prompt so
+        # the agent itself acts defensively before the first user message.
+        try:
+            from hermes_cli.active_sessions import find_concurrent_repo_sessions
+            _repo_root = getattr(self, '_repo_root', None) or _git_repo_root()
+            if _repo_root:
+                _concurrent = find_concurrent_repo_sessions(_repo_root, self.session_id)
+                if _concurrent:
+                    _ids = ', '.join(e.get('session_id', '?')[:20] for e in _concurrent)
+                    self._console_print(
+                        f'[bold yellow]⚠  Concurrent session(s) detected in this repo:[/] {_ids}\n'
+                        f'[yellow]   Both sessions share the same working tree. '
+                        f'Use [bold]hermes -w[/bold] (--worktree) to isolate each session on its own branch.[/]'
+                    )
+                    _note = _build_concurrent_sessions_note(_concurrent)
+                    if _note:
+                        self.system_prompt = ((self.system_prompt or '') + '\n\n' + _note).strip()
+        except Exception:
+            pass
         # Surface any active supply-chain security advisories right after the
         # welcome banner. Quiet/single-query paths call this themselves.
         self._show_security_advisories()
@@ -13756,6 +13838,21 @@ def _signal_handler_q(signum, frame):
     if query or image:
         if not cli._claim_active_session("cli", stderr=bool(quiet)):
             sys.exit(1)
+        # Concurrent-session check for single-query / piped mode.
+        # Uses stderr so the stdout output stays clean for downstream consumers.
+        try:
+            from hermes_cli.active_sessions import find_concurrent_repo_sessions
+            _sq_repo = getattr(cli, '_repo_root', None) or _git_repo_root()
+            if _sq_repo:
+                _sq_concurrent = find_concurrent_repo_sessions(_sq_repo, cli.session_id)
+                if _sq_concurrent:
+                    _sq_ids = ', '.join(e.get('session_id', '?')[:20] for e in _sq_concurrent)
+                    print(f'⚠  Concurrent Hermes session(s) in this repo: {_sq_ids}', file=sys.stderr)
+                    _note = _build_concurrent_sessions_note(_sq_concurrent)
+                    if _note:
+                        cli.system_prompt = ((cli.system_prompt or '') + '\n\n' + _note).strip()
+        except Exception:
+            pass
         try:
             query, single_query_images = _collect_query_images(query, image)
             # Kanban workers spawn with ``hermes chat -q "work kanban task <id>"``;
diff --git a/hermes_cli/active_sessions.py b/hermes_cli/active_sessions.py
index 7fdb9c2d7297..faae50ef6576 100644
--- a/hermes_cli/active_sessions.py
+++ b/hermes_cli/active_sessions.py
@@ -78,7 +78,18 @@ def active_session_limit_message(active_count: int, max_sessions: int) -> str:
 
 
 def _state_dir() -> Path:
-    return get_hermes_home() / "runtime"
+    # Allow an explicit override for CI and container setups.
+    override = os.environ.get("HERMES_SESSIONS_STATE", "").strip()
+    if override:
+        return Path(override)
+    # Anchor to the *installation root* rather than the active profile home so
+    # that Desktop, WebUI, and CLI sessions — which may each have a different
+    # $HERMES_HOME when profiles are in use — all write to the same registry.
+    try:
+        from hermes_constants import get_default_hermes_root
+        return get_default_hermes_root() / "runtime"
+    except Exception:
+        return get_hermes_home() / "runtime"
 
 
 def _state_path() -> Path:
@@ -318,3 +329,32 @@ def active_session_registry_snapshot() -> list[dict[str, Any]]:
         entries = _prune_dead(_read_entries(state_path))
         _write_entries(state_path, entries)
         return entries
+
+
+def find_concurrent_repo_sessions(
+    repo_root: str,
+    our_session_id: str,
+) -> list[dict[str, Any]]:
+    """Return live sessions sharing the same git repository, excluding ours.
+
+    Used to warn the user (and the agent) that another Hermes session is
+    already active in the same working tree so they can avoid clobbering
+    each other's uncommitted changes.
+
+    Returns an empty list when no concurrency is detected or the registry
+    is unavailable — callers must never fail if this function raises.
+    """
+    if not repo_root:
+        return []
+    try:
+        state_path = _state_path()
+        with _FileLock(_lock_path()):
+            entries = _prune_dead(_read_entries(state_path))
+            _write_entries(state_path, entries)
+        return [
+            entry for entry in entries
+            if entry.get("session_id") != our_session_id
+            and (entry.get("metadata") or {}).get("repo_root") == repo_root
+        ]
+    except Exception:
+        return []
diff --git a/plugins/memory/honcho/__init__.py b/plugins/memory/honcho/__init__.py
index 3d130293377b..270ba797f14f 100644
--- a/plugins/memory/honcho/__init__.py
+++ b/plugins/memory/honcho/__init__.py
@@ -440,23 +440,34 @@ def _do_session_init(self, cfg, session_id: str, **kwargs) -> None:
         session = self._manager.get_or_create(self._session_key)
 
         # ----- B6: Memory file migration (one-time, for new sessions) -----
-        # Skip under per-session strategy: every Hermes run creates a fresh
-        # Honcho session by design, so uploading MEMORY.md/USER.md/SOUL.md to
-        # each one would flood the backend with short-lived duplicates instead
-        # of performing a one-time migration.
+        # With per-directory strategy: migrate once per new session (safe, idempotent).
+        # With per-session strategy: every Hermes run is a fresh session, so migrating
+        # on every start would flood the Honcho backend with duplicates.  Instead we
+        # migrate exactly once (first run after install) and mark it with a marker file.
         try:
-            if not session.messages and cfg.session_strategy != "per-session":
+            if session.messages:
+                pass  # existing session — nothing to migrate
+            elif cfg.session_strategy != "per-session":
                 from hermes_constants import get_hermes_home
-                mem_dir = str(get_hermes_home() / "memories")
-                self._manager.migrate_memory_files(self._session_key, mem_dir)
-                logger.debug("Honcho memory file migration attempted for new session: %s", self._session_key)
-            elif cfg.session_strategy == "per-session":
-                logger.debug(
-                    "Honcho memory file migration skipped: per-session strategy creates a fresh session per run (%s)",
-                    self._session_key,
-                )
+                _hermes_home = get_hermes_home()
+                self._manager.migrate_memory_files(self._session_key, str(_hermes_home / "memories"))
+                logger.debug("Honcho memory migration attempted for new session: %s", self._session_key)
+            else:
+                from hermes_constants import get_hermes_home
+                _hermes_home = get_hermes_home()
+                _marker = _hermes_home / ".honcho-memory-migrated"
+                if _marker.exists():
+                    logger.debug("Honcho memory migration skipped: already done (%s)", self._session_key)
+                else:
+                    migrated = self._manager.migrate_memory_files(self._session_key, str(_hermes_home / "memories"))
+                    if migrated:
+                        try:
+                            _marker.touch()
+                        except Exception:
+                            pass
+                    logger.debug("Honcho memory migration (one-time) for %s", self._session_key)
         except Exception as e:
-            logger.debug("Honcho memory file migration skipped: %s", e)
+            logger.debug("Honcho memory migration skipped: %s", e)
 
         # ----- B7: Pre-warming at init -----
         # Context prewarm warms peer.context() (base layer), consumed via
@@ -550,26 +561,35 @@ def _format_first_turn_context(self, ctx: dict) -> str:
         """Format the prefetch context dict into a readable system prompt block."""
         parts = []
 
-        # Session summary — session-scoped context, placed first for relevance
+        # Session summary is session-scoped: it only reflects the current run.
+        # We tag it with the session key so the agent can distinguish it from
+        # the peer-level sections that span multiple sessions (see note below).
         summary = ctx.get("summary", "")
         if summary:
-            parts.append(f"## Session Summary\n{summary}")
+            session_tag = f" [session: {self._session_key}]" if self._session_key else ""
+            parts.append(f"## Session Summary{session_tag}\n{summary}")
+
+        # Peer-level sections (representation, card) are aggregated by Honcho
+        # across ALL sessions for this peer — the Honcho API does not expose a
+        # per-session filter for these fields.  The note makes that explicit so
+        # the agent doesn't treat cross-session observations as current-run facts.
+        _peer_scope = "*(aggregated across all sessions — not limited to the current one)*"
 
         rep = ctx.get("representation", "")
         if rep:
-            parts.append(f"## User Representation\n{rep}")
+            parts.append(f"## User Representation {_peer_scope}\n{rep}")
 
         card = ctx.get("card", "")
         if card:
-            parts.append(f"## User Peer Card\n{card}")
+            parts.append(f"## User Peer Card {_peer_scope}\n{card}")
 
         ai_rep = ctx.get("ai_representation", "")
         if ai_rep:
-            parts.append(f"## AI Self-Representation\n{ai_rep}")
+            parts.append(f"## AI Self-Representation {_peer_scope}\n{ai_rep}")
 
         ai_card = ctx.get("ai_card", "")
         if ai_card:
-            parts.append(f"## AI Identity Card\n{ai_card}")
+            parts.append(f"## AI Identity Card {_peer_scope}\n{ai_card}")
 
         if not parts:
             return ""
diff --git a/plugins/memory/honcho/client.py b/plugins/memory/honcho/client.py
index df8c839aa817..da197c3145ab 100644
--- a/plugins/memory/honcho/client.py
+++ b/plugins/memory/honcho/client.py
@@ -368,8 +368,11 @@ class HonchoClientConfig:
     user_observe_others: bool = True
     ai_observe_me: bool = True
     ai_observe_others: bool = True
-    # Session resolution
-    session_strategy: str = "per-directory"
+    # Session resolution.
+    # "per-session" gives every Hermes run its own isolated Honcho session,
+    # which prevents memory cross-bleed when two sessions share a directory.
+    # Set "per-directory" explicitly to persist context across runs in a project.
+    session_strategy: str = "per-session"
     session_peer_prefix: bool = False
     sessions: dict[str, str] = field(default_factory=dict)
     # Raw global config for anything else consumers need
@@ -493,7 +496,7 @@ def from_global_config(
         # sessionStrategy / sessionPeerPrefix: host first, root fallback
         session_strategy = (
             host_block.get("sessionStrategy")
-            or raw.get("sessionStrategy", "per-directory")
+            or raw.get("sessionStrategy", "per-session")
         )
         host_prefix = host_block.get("sessionPeerPrefix")
         session_peer_prefix = (
diff --git a/tests/honcho_plugin/test_client.py b/tests/honcho_plugin/test_client.py
index 7e956aa54c30..b488ef8e0140 100644
--- a/tests/honcho_plugin/test_client.py
+++ b/tests/honcho_plugin/test_client.py
@@ -31,7 +31,7 @@ def test_default_values(self):
         assert config.timeout is None
         assert config.enabled is False
         assert config.save_messages is True
-        assert config.session_strategy == "per-directory"
+        assert config.session_strategy == "per-session"
         assert config.recall_mode == "hybrid"
         assert config.session_peer_prefix is False
         assert config.sessions == {}
@@ -167,7 +167,7 @@ def test_session_strategy_default_from_global_config(self, tmp_path):
         config_file = tmp_path / "config.json"
         config_file.write_text(json.dumps({"apiKey": "***"}))
         config = HonchoClientConfig.from_global_config(config_path=config_file)
-        assert config.session_strategy == "per-directory"
+        assert config.session_strategy == "per-session"
 
     def test_context_tokens_default_is_none(self, tmp_path):
         """Default context_tokens should be None (uncapped) unless explicitly set."""