Merge branch 'main' into doc-skill-callouts

docs/tools/mcp-server.md

@@ -735,6 +735,43 @@ tools. The model will automatically:
 
 The MCP integration tracks several states:
 
+#### Overriding extension configurations
+
+If an MCP server is provided by an extension (for example, the
+`google-workspace` extension), you can still override its settings in your local
+`settings.json`. Gemini CLI merges your local configuration with the extension's
+defaults:
+
+- **Tool lists:** Tool lists are merged securely to ensure the most restrictive
+  policy wins:
+  - **Exclusions (`excludeTools`):** Arrays are combined (unioned). If either
+    source blocks a tool, it remains disabled.
+  - **Inclusions (`includeTools`):** Arrays are intersected. If both sources
+    provide an allowlist, only tools present in **both** lists are enabled. If
+    only one source provides an allowlist, that list is respected.
+  - **Precedence:** `excludeTools` always takes precedence over `includeTools`.
+
+  This ensures you always have veto power over tools provided by an extension
+  and that an extension cannot re-enable tools you have omitted from your
+  personal allowlist.
+
+- **Environment variables:** The `env` objects are merged. If the same variable
+  is defined in both places, your local value takes precedence.
+- **Scalar properties:** Properties like `command`, `url`, and `timeout` are
+  replaced by your local values if provided.
+
+**Example override:**
+
+```json
+{
+  "mcpServers": {
+    "google-workspace": {
+      "excludeTools": ["gmail.send"]
+    }
+  }
+}
+```
+
 #### Server status (`MCPServerStatus`)
 
 - **`DISCONNECTED`:** Server is not connected or has errors

docs/tools/shell.md

@@ -120,6 +120,14 @@ tools to detect if they are being run from within the Gemini CLI.
 
 ## Command restrictions
 
+<!-- prettier-ignore -->
+> [!WARNING]
+> The `tools.core` setting is an **allowlist for _all_ built-in
+> tools**, not just shell commands. When you set `tools.core` to any value,
+> _only_ the tools explicitly listed will be enabled. This includes all built-in
+> tools like `read_file`, `write_file`, `glob`, `grep_search`, `list_directory`,
+> `replace`, etc.
+
 You can restrict the commands that can be executed by the `run_shell_command`
 tool by using the `tools.core` and `tools.exclude` settings in your
 configuration file.