Keep fixed values when an MCP server's tools are refreshed or re-saved

Parameters that still exist after re-reading the server keep the value the
user fixed; parameters the server dropped go with the old schema.

docsgpt/api/user/tools/mcp.py

@@ -5,6 +5,7 @@ from urllib.parse import urlencode, urlparse
 from flask import current_app, jsonify, make_response, redirect, request
 from flask_restx import Namespace, Resource, fields
 
+from docsgpt.agents.tool_pins import carry_pins_between
 from docsgpt.agents.tools.mcp_tool import MCPOAuthManager, MCPTool
 from docsgpt.api import api
 from docsgpt.api.user.tools.routes import transform_actions
@@ -414,7 +415,8 @@ class MCPServerSave(Resource):
                             "custom_name": display_name,
                             "description": description,
                             "config": storage_config,
-                            "actions": transformed_actions,
+                            # Fixed values the user set survive a re-save.
+                            "actions": carry_pins_between(existing_doc.get("actions"), transformed_actions),
                             "status": status_bool,
                             "connection_id": connection_id,
                         },
@@ -442,7 +444,7 @@ class MCPServerSave(Resource):
                                 "custom_name": display_name,
                                 "description": description,
                                 "config": storage_config,
-                                "actions": transformed_actions,
+                                "actions": carry_pins_between(existing_by_name.get("actions"), transformed_actions),
                                 "status": status_bool,
                                 "connection_id": connection_id,
                             },

docsgpt/connectors/mcp.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+from docsgpt.agents.tool_pins import carry_pins
 from docsgpt.connectors import catalog, service
 from docsgpt.connectors.permissions import apply_default_permissions
 from docsgpt.storage.db.repositories.connector_sessions import ConnectorSessionsRepository
@@ -43,9 +44,10 @@ def discover_builtin_actions(user_id: str, connection: dict) -> list[dict]:
 def refresh_mcp_tools(user_id: str, connection: dict) -> dict:
     """Re-read the actions of every MCP tool on a connection.
 
-    Actions that still exist keep the permissions the user chose; new ones
-    get the defaults from their annotations (reads always allowed, writes
-    need approval); removed ones disappear.
+    Actions that still exist keep the permissions the user chose and the
+    fixed values of parameters they still have; new ones get the defaults
+    from their annotations (reads always allowed, writes need approval);
+    removed ones disappear.
 
     Returns:
         ``{"added": [...], "removed": [...], "tools": [...]}``.
@@ -64,7 +66,7 @@ def refresh_mcp_tools(user_id: str, connection: dict) -> dict:
             old = previous.get(action.get("name"))
             if old is not None:
                 action = {
-                    **action,
+                    **carry_pins(old, action),
                     "active": old.get("active", True),
                     "require_approval": bool(old.get("require_approval")),
                 }

tests/api/user/test_tools_mcp_pg.py

@@ -404,6 +404,47 @@ class TestMCPServerSave:
             response = MCPServerSave().post()
         assert response.status_code in (200, 201)
 
+    def test_saving_an_existing_server_keeps_fixed_values(self, app, pg_conn):
+        from docsgpt.api.user.tools.mcp import MCPServerSave
+        from docsgpt.storage.db.repositories.user_tools import UserToolsRepository
+
+        user = "u-mcp-resave"
+        repo = UserToolsRepository(pg_conn)
+        existing = repo.create(
+            user, "mcp_tool",
+            config={"server_url": "https://example.com/mcp", "auth_type": "none"},
+            display_name="My MCP",
+            actions=[{
+                "name": "search",
+                "active": True,
+                "parameters": {"properties": {
+                    "q": {"type": "string", "filled_by_llm": True, "value": ""},
+                    "team": {"type": "string", "filled_by_llm": False, "value": "ENG"},
+                }},
+            }],
+        )
+        fake_tool = MagicMock()
+        fake_tool.get_actions_metadata.return_value = [{
+            "name": "search",
+            "parameters": {"properties": {"q": {"type": "string"}, "team": {"type": "string"}}},
+        }]
+        with _patch_db(pg_conn), patch(
+            "docsgpt.api.user.tools.mcp.MCPTool", return_value=fake_tool,
+        ), app.test_request_context(
+            "/api/mcp_server/save", method="POST",
+            json={
+                "id": str(existing["id"]),
+                "displayName": "My MCP",
+                "config": {"transport_type": "http", "server_url": "https://example.com/mcp", "auth_type": "none"},
+            },
+        ):
+            from flask import request
+            request.decoded_token = {"sub": user}
+            response = MCPServerSave().post()
+        assert response.status_code == 200
+        team = repo.get_any(str(existing["id"]), user)["actions"][0]["parameters"]["properties"]["team"]
+        assert team["filled_by_llm"] is False and team["value"] == "ENG"
+
 
 class TestMCPOAuthCallback:
     def test_error_param_redirects_error(self, app):

tests/connectors/test_mcp_refresh.py

@@ -81,6 +81,27 @@ class TestRefresh:
         assert actions["create_issue"]["parameters"]["properties"]["q"]["filled_by_llm"] is True
         assert [t["id"] for t in result["tools"]] == [tool_id]
 
+    def test_fixed_values_survive_for_parameters_that_still_exist(self, pg_conn):
+        connection = _connection(pg_conn)
+        pinned = _action("search_issues")
+        pinned["parameters"]["properties"] = {
+            "q": {"type": "string", "filled_by_llm": True, "value": ""},
+            "team": {"type": "string", "filled_by_llm": False, "value": "ENG"},
+            "gone": {"type": "string", "filled_by_llm": False, "value": "x"},
+        }
+        tool_id = _tool(pg_conn, connection["id"], [pinned])
+        fresh = _action("search_issues")
+        fresh["parameters"]["properties"] = {"q": {"type": "string"}, "team": {"type": "string"}}
+        with _db(pg_conn), patch.object(mcp, "_discover", return_value=[fresh]):
+            mcp.refresh_mcp_tools("alice", connection)
+        action = pg_conn.execute(
+            text("SELECT actions FROM user_tools WHERE id = CAST(:i AS uuid)"), {"i": tool_id}
+        ).scalar()[0]
+        properties = action["parameters"]["properties"]
+        assert properties["team"] == {"type": "string", "filled_by_llm": False, "value": "ENG"}
+        assert properties["q"]["filled_by_llm"] is True
+        assert "gone" not in properties
+
     def test_other_tools_on_the_connection_are_left_alone(self, pg_conn):
         connection = _connection(pg_conn)
         pg_conn.execute(