Stabilize Claude MCP and lighten runner

Author: PsYcGoD

README.md

@@ -35,7 +35,7 @@ SAGE is available through both Python and npm entry points. The npm package dele
 | MCP Registry | [`io.github.PsYcGoD/sage`](https://registry.modelcontextprotocol.io/) | Official registry entry |
 | Glama | [`PsYcGoD/sage`](https://glama.ai/mcp/servers/PsYcGoD/sage) | Listed MCP server |
 
-MCP stdio servers exit after 10 seconds of inactivity by default. Set `SAGE_MCP_IDLE_TIMEOUT_SECONDS` to a higher value if a client needs a longer idle window.
+MCP stdio servers exit after 5 minutes of inactivity by default. The ML daemon still sleeps after short idle windows; MCP stays alive longer because clients such as Claude Code keep stdio servers open between tool calls. Set `SAGE_MCP_IDLE_TIMEOUT_SECONDS` for a stricter or longer local policy.
 
 ### Proof at Full Context
 

js/src/mcp/server.ts

@@ -7,7 +7,7 @@ import {
 } from '@modelcontextprotocol/sdk/types.js';
 import { TOOLS, handleToolCall } from './tools.js';
 
-const DEFAULT_IDLE_TIMEOUT_MS = 10_000;
+const DEFAULT_IDLE_TIMEOUT_MS = 300_000;
 const MIN_IDLE_TIMEOUT_MS = 10_000;
 
 function getIdleTimeoutMs(): number {

src/sage/mcp/server.py

@@ -40,7 +40,7 @@
 PROTOCOL_VERSION = "2024-11-05"
 SERVER_INFO = {"name": "sage", "version": "2.0.4"}
 COMMAND_TOOL_NAMES = {"sage_run_command"}
-DEFAULT_IDLE_TIMEOUT_SECONDS = 10
+DEFAULT_IDLE_TIMEOUT_SECONDS = 300
 MIN_IDLE_TIMEOUT_SECONDS = 10
 
 
@@ -49,8 +49,10 @@ def _mcp_idle_timeout() -> int:
 
     MCP clients usually restart stdio servers on demand, so idle MCP servers
     should not sit around forever when an AI client crashes or forgets to close
-    stdin. The default matches SAGE's low-footprint daemon policy and can be
-    raised by setting SAGE_MCP_IDLE_TIMEOUT_SECONDS.
+    stdin. MCP clients such as Claude Code often keep a stdio server open
+    between tool calls, so the default must be long enough not to look like a
+    flaky server while still cleaning truly abandoned processes. Set
+    SAGE_MCP_IDLE_TIMEOUT_SECONDS for stricter or longer local policy.
     """
     raw = os.getenv("SAGE_MCP_IDLE_TIMEOUT_SECONDS", "").strip()
     if not raw:

src/sage/ml/family_model.py

@@ -12,10 +12,12 @@
 from datetime import datetime, timezone
 from pathlib import Path
 from typing import Any
+import warnings
 
 import joblib
 import pandas as pd
 from sklearn.ensemble import ExtraTreesClassifier, GradientBoostingClassifier, RandomForestClassifier, VotingClassifier
+from sklearn.exceptions import InconsistentVersionWarning
 from sklearn.metrics import accuracy_score
 from sklearn.pipeline import Pipeline
 from sklearn.preprocessing import StandardScaler
@@ -242,7 +244,9 @@ def _load_model(self, path: Path) -> dict[str, Any] | None:
             return None
 
         try:
-            package = joblib.load(path)
+            with warnings.catch_warnings():
+                warnings.simplefilter("ignore", InconsistentVersionWarning)
+                package = joblib.load(path)
             if package.get("version") != MODEL_VERSION:
                 return None
             self._cache[cache_key] = package

src/sage/ml/model.py

@@ -6,10 +6,12 @@
 from datetime import datetime, timezone
 from pathlib import Path
 from typing import Any
+import warnings
 
 import joblib
 import pandas as pd
 from sklearn.ensemble import ExtraTreesClassifier, GradientBoostingClassifier, HistGradientBoostingClassifier, RandomForestClassifier, VotingClassifier
+from sklearn.exceptions import InconsistentVersionWarning
 from sklearn.metrics import accuracy_score, precision_score, recall_score, roc_auc_score
 from sklearn.model_selection import train_test_split
 from sklearn.pipeline import Pipeline
@@ -188,7 +190,9 @@ def load(self) -> dict[str, Any] | None:
         if not self.model_path.exists():
             return None
         try:
-            package = joblib.load(self.model_path)
+            with warnings.catch_warnings():
+                warnings.simplefilter("ignore", InconsistentVersionWarning)
+                package = joblib.load(self.model_path)
         except Exception:
             return None
         if package.get("version") != MODEL_VERSION:

src/sage/runner.py

@@ -326,7 +326,15 @@ def enqueue_stream(stream, stream_name: str) -> None:
     )
 
     agent_results = []
-    if os.environ.get("SAGE_DISABLE_AGENTS") != "1":
+    agents_enabled = (
+        os.environ.get("SAGE_ENABLE_AGENTS") == "1"
+        or (
+            returncode != 0
+            and os.environ.get("SAGE_DISABLE_FAILURE_AGENTS") != "1"
+            and os.environ.get("SAGE_DISABLE_AGENTS") != "1"
+        )
+    )
+    if agents_enabled:
         try:
             from .agents import execute_agents_for_run
 
@@ -429,12 +437,12 @@ def _run_agents_background():
         if result['token_savings'] > 0:
             print(f"[sage] context: saved {result['token_savings']} tokens ({result['compression_ratio']} compression)")
 
-        if os.environ.get("SAGE_DISABLE_AGENTS") != "1":
+        if agents_enabled:
             from .agents.registry import select_agents_for_command
             specs = select_agents_for_command(command_text)
             if specs:
                 agent_names = ", ".join(s.name for s in specs)
-                print(f"[sage] agents: {len(specs)} completed ({agent_names})")
+                print(f"[sage] agents: {len(specs)} queued ({agent_names})")
 
     if not suppress_summary:
         print("[sage] summary:")

tests/test_mcp_sage_tools.py

@@ -34,7 +34,7 @@ def test_mcp_run_command_is_opt_in(monkeypatch):
 
 def test_mcp_idle_timeout_is_configurable_and_clamped(monkeypatch):
     monkeypatch.delenv("SAGE_MCP_IDLE_TIMEOUT_SECONDS", raising=False)
-    assert _mcp_idle_timeout() == 10
+    assert _mcp_idle_timeout() == 300
 
     monkeypatch.setenv("SAGE_MCP_IDLE_TIMEOUT_SECONDS", "2")
     assert _mcp_idle_timeout() == 10
@@ -43,7 +43,7 @@ def test_mcp_idle_timeout_is_configurable_and_clamped(monkeypatch):
     assert _mcp_idle_timeout() == 45
 
     monkeypatch.setenv("SAGE_MCP_IDLE_TIMEOUT_SECONDS", "bad")
-    assert _mcp_idle_timeout() == 10
+    assert _mcp_idle_timeout() == 300
 
 
 def test_external_mcp_missing_command_fails_fast():