nexo-brain 7.36.0 → 7.37.1

package/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "nexo-brain",
-  "version": "7.36.0",
+  "version": "7.37.1",
   "description": "Local cognitive runtime for Claude Code \u2014 persistent memory, overnight learning, doctor diagnostics, personal scripts, recovery-aware jobs, startup preflight, and optional dashboard/power helper.",
   "author": {
     "name": "NEXO Brain",

package/README.md

@@ -18,7 +18,7 @@
 
 [Watch the overview video](https://nexo-brain.com/watch/) · [Watch on YouTube](https://www.youtube.com/watch?v=i2lkGhKyVqI) · [Open the infographic](https://nexo-brain.com/assets/nexo-brain-infographic-v5.png)
 
-Version `7.36.0` is the current packaged-runtime line. Minor release - local index disk reclaim: the local file/code index (`local-context.db`) no longer grows without bound. It now uses `auto_vacuum=INCREMENTAL` plus a one-time guarded `VACUUM` to convert existing databases, stores embeddings as compact float32 BLOBs instead of JSON text (~4-6x smaller, back-compatible dual-write/dual-read with a resumable backfill and kill switches), reclaims disk on purge/clear, and the daily self-audit now actively compacts at its size cap (`NEXO_LOCAL_INDEX_MAX_BYTES`) instead of only warning. An established index reclaims ~10-20GB immediately and grows several-fold slower; the backup subsystem was audited and is already bounded. Builds on v7.35.0 (selective forget + recurring-incident diagnostic templates).
+Version `7.37.1` is the current packaged-runtime line. Patch release over v7.37.0 - release hardening for Desktop-bundled Brain: large existing `local-context.db` files no longer run a surprise full `VACUUM` on the first writer, `schema_abstraction` MCP tools are loaded by the essential startup set, and learning tools tolerate Desktop compatibility payloads. Builds on v7.37.0 (transparent server self-heal + email zombie reinjection guard).
 
 Previously in `7.31.9`: patch release over v7.31.8 - UI release closeout now has to prove the original reported symptom was reopened with observable evidence before claiming the release is ready.
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nexo-brain",
-  "version": "7.36.0",
+  "version": "7.37.1",
   "mcpName": "io.github.wazionapps/nexo",
   "description": "NEXO Brain — Shared brain for AI agents. Persistent memory, semantic RAG, natural forgetting, metacognitive guard, trust scoring, 150+ MCP tools. Works with Claude Code, Codex, Claude Desktop & any MCP client. 100% local, free.",
   "homepage": "https://nexo-brain.com",

package/src/local_context/db.py

@@ -20,6 +20,8 @@ MAIN_CLEANUP_STATE_KEY = "local_context_main_tables_drained"
 # per never-converted DB (guarded by free disk) and record it here so it never
 # re-runs the expensive rewrite. See ensure_local_context_db().
 AUTO_VACUUM_CONVERTED_KEY = "auto_vacuum_converted"
+AUTO_VACUUM_MAX_SYNC_BYTES_ENV = "NEXO_LOCAL_CONTEXT_AUTO_VACUUM_MAX_SYNC_BYTES"
+DEFAULT_AUTO_VACUUM_MAX_SYNC_BYTES = 128 * 1024 * 1024
 
 LOCAL_CONTEXT_TABLES: tuple[str, ...] = (
     "local_index_roots",
@@ -472,6 +474,9 @@ def _convert_auto_vacuum_once(conn: sqlite3.Connection, db_path: Path) -> None:
             free = shutil.disk_usage(db_path.parent).free
         except OSError:
             return
+        max_sync_bytes = _auto_vacuum_max_sync_bytes()
+        if max_sync_bytes <= 0 or db_size > max_sync_bytes:
+            return
         if free <= db_size * 2:
             # Not enough scratch room — leave NONE mode, retry on a later boot.
             return
@@ -486,6 +491,16 @@ def _convert_auto_vacuum_once(conn: sqlite3.Connection, db_path: Path) -> None:
         pass
 
 
+def _auto_vacuum_max_sync_bytes() -> int:
+    value = os.environ.get(AUTO_VACUUM_MAX_SYNC_BYTES_ENV, "")
+    if value:
+        try:
+            return max(0, int(value))
+        except (TypeError, ValueError):
+            return DEFAULT_AUTO_VACUUM_MAX_SYNC_BYTES
+    return DEFAULT_AUTO_VACUUM_MAX_SYNC_BYTES
+
+
 def get_local_context_db() -> sqlite3.Connection:
     ensure_local_context_db()
     assert _CONN is not None

package/src/runtime_versioning.py

@@ -1130,15 +1130,128 @@ def prime_process_fingerprint() -> str:
 _DRIFT_AUTOEXIT_SCHEDULED = False
 _DRIFT_EXIT_CODE = 75
 _DRIFT_EXIT_DELAY_SECONDS = 0.5
+# Anti crash-loop: cap how many times one process-chain may self-heal-reexec
+# before giving up and falling back to a plain exit. A half-written update or
+# an unreadable tree must never thrash.
+_SELFHEAL_MAX_GENERATIONS = 3
+# Tool calls currently executing: never re-exec mid-request (would desync the
+# JSON-RPC stream of a sibling call). Incremented/decremented in on_call_tool.
+_INFLIGHT_TOOL_CALLS = 0
+_DRIFT_REEXEC_DEFER_MAX = 20
+_drift_reexec_defers = 0
 
 
-def _request_drift_exit() -> None:
+def _selfheal_reexec_disabled() -> bool:
+    return str(os.environ.get("NEXO_DISABLE_SELFHEAL_REEXEC", "") or "").strip().lower() in {"1", "true", "yes"}
+
+
+def _running_as_resident_service() -> bool:
+    # The resident HTTP runtime-service serves multiple clients and has its own
+    # self-retire (start_resident_obsolescence_watch). It must NOT execv. Lazy
+    # import to avoid a circular import; fall back to an env sentinel.
+    try:
+        from runtime_service import is_runtime_service_process
+
+        return bool(is_runtime_service_process())
+    except Exception:
+        return str(os.environ.get("NEXO_RUNTIME_SERVICE", "") or "").strip().lower() in {"1", "true", "yes"}
+
+
+def _selfheal_teardown() -> None:
+    """Release SQLite/WAL handles before re-exec so the new image does not fight
+    its own locks. Best-effort: a teardown failure must never block the heal."""
+    try:
+        from local_context.db import close_local_context_db
+
+        close_local_context_db()
+    except Exception:
+        pass
+    try:
+        from db import close_db
+
+        close_db()
+    except Exception:
+        pass
+
+
+def _drift_hard_exit() -> None:
+    # Fallback (today's behavior): exit so a relaunching client (e.g. Claude
+    # Code) spawns a fresh process on the new code. Used when re-exec can't run.
     try:
         os._exit(_DRIFT_EXIT_CODE)
     except Exception:
         os._exit(1)
 
 
+def _request_drift_exit() -> None:
+    """Heal a post-update fingerprint drift TRANSPARENTLY: re-exec the live
+    process in place (os.execv -> same PID, same inherited stdio pipes to the
+    MCP client) so it loads the new code on disk without the client/session
+    breaking and without the user restarting anything. Falls back to a plain
+    exit on any obstacle. FAIL-OPEN: this must never be worse than today's exit.
+    """
+    global _drift_reexec_defers
+    try:
+        # 0. Opt-out / non-posix / resident service -> today's behavior.
+        #    (execv on native Windows spawns+exits, dropping inherited stdio.)
+        if _selfheal_reexec_disabled() or os.name != "posix" or _running_as_resident_service():
+            _drift_hard_exit()
+            return
+
+        # 1. Never re-exec mid tool-call: defer until in-flight calls drain.
+        if _INFLIGHT_TOOL_CALLS > 0 and _drift_reexec_defers < _DRIFT_REEXEC_DEFER_MAX:
+            _drift_reexec_defers += 1
+            try:
+                loop = asyncio.get_running_loop()
+                loop.call_later(_DRIFT_EXIT_DELAY_SECONDS, _request_drift_exit)
+                return
+            except RuntimeError:
+                pass  # no running loop -> proceed to re-exec now
+
+        # 2. Resolve the target fingerprint + anti-loop guards.
+        try:
+            target_fp = installed_runtime_fingerprint(use_cache=False) or ""
+        except Exception:
+            target_fp = ""
+        already_healed_target = bool(target_fp) and os.environ.get("NEXO_SELFHEAL_GEN", "") == target_fp[:16]
+        try:
+            count = int(os.environ.get("NEXO_SELFHEAL_COUNT", "0") or "0")
+        except ValueError:
+            count = 0
+        # We already re-exec'd toward this exact target (or hit the cap) and STILL
+        # drift -> the update is broken/unstable; stop looping, exit once so a
+        # relaunching client gets a clean process; a non-relaunching client keeps
+        # the stale-but-alive server returning mcp_restart_required.
+        if already_healed_target or count >= _SELFHEAL_MAX_GENERATIONS:
+            _drift_hard_exit()
+            return
+
+        # 3. Resolve the new entrypoint (the active snapshot's server.py).
+        server_path = ""
+        try:
+            candidate = active_runtime_root() / "server.py"
+            if candidate.is_file():
+                server_path = str(candidate)
+        except Exception:
+            server_path = ""
+        if not server_path and len(sys.argv) > 1 and os.path.isfile(sys.argv[1]):
+            server_path = sys.argv[1]
+        if not server_path:
+            _drift_hard_exit()
+            return
+
+        # 4. Best-effort teardown, stamp anti-loop env, re-exec in place.
+        _selfheal_teardown()
+        os.environ["NEXO_SELFHEAL_COUNT"] = str(count + 1)
+        if target_fp:
+            os.environ["NEXO_SELFHEAL_GEN"] = target_fp[:16]
+        argv_tail = sys.argv[2:] if len(sys.argv) > 2 else []
+        os.execv(sys.executable, [sys.executable, server_path, *argv_tail])
+    except Exception:
+        # Fail-open: any failure (execv raised, teardown, platform) -> plain exit.
+        _drift_hard_exit()
+
+
 def _schedule_drift_autoexit() -> None:
     global _DRIFT_AUTOEXIT_SCHEDULED
     if _DRIFT_AUTOEXIT_SCHEDULED:
@@ -1152,6 +1265,25 @@ def _schedule_drift_autoexit() -> None:
     loop.call_later(_DRIFT_EXIT_DELAY_SECONDS, _request_drift_exit)
 
 
+def maybe_selfheal_on_boot(client: str = "") -> bool:
+    """Pre-serve drift check: if a freshly-spawned stdio child already loaded
+    stale code (launched right after an update and would only ever receive
+    allowlisted tools, so the per-call middleware never trips), re-exec into the
+    new code BEFORE serving the first request. Normally does not return (execv
+    replaces the process). Fail-open: any error -> return False and serve as-is.
+    Call only in stdio-child mode (the resident HTTP service self-retires)."""
+    try:
+        state = resolve_restart_required(client=client)
+        if not state.get("restart_required"):
+            return False
+        if state.get("reason") not in ("fingerprint_mismatch", "version_mismatch"):
+            return False
+        _request_drift_exit()
+        return True
+    except Exception:
+        return False
+
+
 @dataclass
 class RestartRequiredMiddleware(Middleware):
     client: str = ""
@@ -1214,11 +1346,18 @@ class RestartRequiredMiddleware(Middleware):
         )
 
     async def on_call_tool(self, context, call_next):
+        global _INFLIGHT_TOOL_CALLS
         tool_name = str(getattr(context.message, "name", "") or "").strip()
         state = resolve_restart_required(client=self.client)
         state = self._ack_current_client_if_restarted(state)
         if not state["restart_required"] or tool_name in RESTART_ALLOWLIST:
-            return await call_next(context)
+            # Track in-flight executions so a drift self-heal re-exec defers until
+            # no tool call is mid-stream (avoids desyncing the JSON-RPC framing).
+            _INFLIGHT_TOOL_CALLS += 1
+            try:
+                return await call_next(context)
+            finally:
+                _INFLIGHT_TOOL_CALLS -= 1
 
         payload = {
             "ok": False,

package/src/scripts/nexo-email-monitor.py

@@ -947,6 +947,131 @@ def _reconcile_finished_rows(conn, *, hours=24):
     return reconciled
 
 
+def _reconcile_replied_zombies(conn):
+    """Close 'processing'/'pending' emails that were ALREADY replied to before
+    the worker session marked them processed.
+
+    Failure mode (self-critiques 1111/1112, 25-may-2026): a worker session
+    sends the reply through ``nexo-send-reply.py`` but dies (exit -9) BEFORE
+    it flips the BD row to a terminal status. The stuck/zombie recovery then
+    resets the row to 'pending' and the daemon reinjects the MID, producing a
+    DUPLICATE reply to the operator.
+
+    This reconciler consults two durable signals that survive a session crash
+    and, if either says the operator was already answered, closes the row as
+    terminal ('processed') and logs a 'resolution' marker instead of letting it
+    be reinjected:
+      1. ``email_events`` lifecycle markers ('replied'/'resolution'/
+         'action_done') written by ``record_reply_lifecycle()`` at send time.
+      2. ``sent_email_events`` rows whose In-Reply-To / References point back at
+         the inbound ``message_id`` (the durable outbound ledger written by
+         ``record_sent_email()``).
+
+    Matching is strictly per inbound message_id, so a fresh message in an
+    already-answered thread (its own distinct MID) never false-positives.
+    """
+    if not _table_exists(conn, "emails"):
+        return []
+
+    cols = _email_table_columns(conn)
+    has_sent_ledger = _table_exists(conn, "sent_email_events")
+
+    rows = conn.execute(
+        """
+        SELECT message_id, subject, status
+        FROM emails
+        WHERE status IN ('processing', 'pending')
+        """
+    ).fetchall()
+
+    sanitized = []
+    for row in rows:
+        mid = row["message_id"]
+        if not mid:
+            continue
+
+        signal = None
+        sent_reference = None
+
+        # Signal 1 — in-DB lifecycle marker keyed to this inbound MID.
+        ev = conn.execute(
+            """
+            SELECT event, MAX(timestamp) AS ts
+            FROM email_events
+            WHERE email_id = ?
+              AND event IN ('replied', 'resolution', 'action_done')
+            """,
+            (mid,),
+        ).fetchone()
+        if ev and ev["ts"]:
+            signal = f"email_event:{ev['event']}"
+            sent_reference = ev["ts"]
+
+        # Signal 2 — durable outbound ledger pointing back at this MID.
+        if signal is None and has_sent_ledger:
+            sent = conn.execute(
+                """
+                SELECT message_id AS sent_mid, sent_at
+                FROM sent_email_events
+                WHERE in_reply_to = ?
+                   OR references_header LIKE '%' || ? || '%'
+                ORDER BY sent_at DESC
+                LIMIT 1
+                """,
+                (mid, mid),
+            ).fetchone()
+            if sent:
+                signal = "sent_email_events"
+                sent_reference = sent["sent_at"]
+
+        if signal is None:
+            continue
+
+        updates = ["status = 'processed'"]
+        if "completed_at" in cols:
+            updates.append(
+                "completed_at = COALESCE(completed_at, datetime('now','localtime'))"
+            )
+        if "error" in cols:
+            updates.append("error = NULL")
+        conn.execute(
+            f"""
+            UPDATE emails
+            SET {', '.join(updates)}
+            WHERE message_id = ?
+              AND status IN ('processing', 'pending')
+            """,
+            (mid,),
+        )
+        _insert_event(
+            conn,
+            mid,
+            "resolution",
+            "Sanitized: reply already sent before BD close (zombie reconcile)",
+            {
+                "reason": "already_replied_reconciled",
+                "previous_status": row["status"],
+                "signal": signal,
+                "sent_reference": sent_reference,
+            },
+        )
+        log.warning(
+            f"Sanitized already-replied zombie email: status={row['status']} "
+            f"signal={signal} subj={(row['subject'] or '')[:40]} [{mid}] — "
+            f"closed as 'processed', not reinjected"
+        )
+        sanitized.append(
+            {
+                "email_id": mid,
+                "subject": row["subject"],
+                "previous_status": row["status"],
+                "signal": signal,
+            }
+        )
+
+    return sanitized
+
+
 def _recent_debt_flagged(conn, email_id, *, hours=6):
     row = conn.execute(
         """
@@ -1153,6 +1278,9 @@ def scan_debt(db_path=EMAIL_DB_PATH, *, max_items=5):
         return ""
     live_reconciled = _reconcile_processing_rows(conn)
     finished_reconciled = _reconcile_finished_rows(conn)
+    # Close already-replied zombies BEFORE the 2h stuck-recovery below resets
+    # them to 'pending', so the daemon never reinjects a MID we already answered.
+    replied_sanitized = _reconcile_replied_zombies(conn)
 
     items = []
     now_label = datetime.now().isoformat(timespec="seconds")
@@ -1278,14 +1406,17 @@ def scan_debt(db_path=EMAIL_DB_PATH, *, max_items=5):
     conn.commit()
     conn.close()
 
-    if not items:
+    if not items and not replied_sanitized:
         return ""
 
-    lines = ["== PENDING EMAIL DEBT DETECTED ==", "Prioritize closing or clarifying these threads before ignoring them:"]
-    for item in items[:max_items]:
-        lines.append(f"- {item['label']} ({item['detail']})")
-    if len(items) > max_items:
-        lines.append(f"- ... and {len(items) - max_items} more item(s)")
+    lines = []
+    if items:
+        lines.append("== PENDING EMAIL DEBT DETECTED ==")
+        lines.append("Prioritize closing or clarifying these threads before ignoring them:")
+        for item in items[:max_items]:
+            lines.append(f"- {item['label']} ({item['detail']})")
+        if len(items) > max_items:
+            lines.append(f"- ... and {len(items) - max_items} more item(s)")
     if recovered:
         lines.append("")
         lines.append(f"Auto-recovery applied: {len(recovered)} processing-stuck email(s) were reset to pending.")
@@ -1294,6 +1425,12 @@ def scan_debt(db_path=EMAIL_DB_PATH, *, max_items=5):
         lines.append(
             f"Reconciled {len(sent_reconciled)} processing email(s) with already-sent reply events; no re-open applied."
         )
+    if replied_sanitized:
+        lines.append("")
+        lines.append(
+            f"Sanitized {len(replied_sanitized)} already-replied email(s): closed as 'processed' "
+            f"to prevent duplicate operator replies (no reinjection)."
+        )
     total_reconciled = len(live_reconciled) + len(finished_reconciled)
     if total_reconciled:
         lines.append(f"Reconciled {total_reconciled} email(s) with inconsistent lifecycle state.")

package/src/server.py

@@ -139,6 +139,7 @@ from tools_api_call import (
 from runtime_versioning import (
     RestartRequiredMiddleware,
     build_mcp_status,
+    maybe_selfheal_on_boot,
     prime_process_fingerprint,
     prime_process_version,
 )
@@ -339,6 +340,7 @@ _ESSENTIAL_MCP_STARTUP_PLUGINS = (
     "preferences.py",
     "protocol.py",
     "recover.py",
+    "schema_abstraction.py",
     "skills.py",
     "user_state_tools.py",
     "workflow.py",
@@ -2629,12 +2631,14 @@ def nexo_learning_resolve_candidate(
 
 
 @mcp.tool
-def nexo_learning_search(query: str, category: str = "") -> str:
+def nexo_learning_search(query: str, category: str = "", limit: int = 0) -> str:
     """Search learnings by keyword. Searches title and content.
 
     Args:
         query: Search term.
         category: Filter by category (optional).
+        limit: Accepted for Desktop/client compatibility; search ranking is
+            owned by the Brain handler.
     """
     return handle_learning_search(query, category)
 
@@ -2766,13 +2770,15 @@ def nexo_learning_delete(id: int) -> str:
 
 
 @mcp.tool
-def nexo_learning_list(category: str = "", created_after: str = "", created_before: str = "") -> str:
+def nexo_learning_list(category: str = "", created_after: str = "", created_before: str = "", limit: int = 0) -> str:
     """List all learnings, grouped by category.
 
     Args:
         category: Filter by category (optional). If empty, shows all grouped.
         created_after: Filter to learnings created at or after this date/time (optional).
         created_before: Filter to learnings created at or before this date/time (optional).
+        limit: Accepted for Desktop/client compatibility; grouping is owned by
+            the Brain handler.
     """
     return handle_learning_list(category, created_after, created_before)
 
@@ -3264,4 +3270,10 @@ if __name__ == "__main__":
                 port=port,
                 on_exit=lambda: (close_local_context_db(), close_db()),
             )
+        else:
+            # stdio child: if we booted already-stale (spawned right after an
+            # update), re-exec into the new code transparently before serving —
+            # covers the case where only allowlisted tools are called and the
+            # per-call drift middleware would never trip. Fail-open.
+            maybe_selfheal_on_boot(client=str(os.environ.get("NEXO_MCP_CLIENT", "") or "").strip())
         mcp.run(**run_kwargs)