Update docs for run --from-config (#163)

Signed-off-by: lujunsan <[email protected]>
Signed-off-by: Dan Barr <[email protected]>
Co-authored-by: Dan Barr <[email protected]>

Author: lujunsan

docs/toolhive/guides-cli/run-mcp-servers.mdx

@@ -805,6 +805,13 @@ This creates a new server instance with identical settings to the original. If
 the original server used secrets, you must have the same secrets available in
 your ToolHive secrets store.
 
+:::note
+
+When you use `--from-config`, you cannot specify any other command-line flags.
+The configuration file must contain all server settings.
+
+:::
+
 ## Next steps
 
 See [Monitor and manage MCP servers](./manage-mcp-servers.md) to monitor and