agent: Use standardized MCP configuration format in settings (#33539)

Changes our MCP settings from:

```json
{
  "context_servers": {
    "some-mcp-server": {
      "source": "custom",
      "command": {
        "path": "npx",
        "args": [
          "-y",
          "@supabase/mcp-server-supabase@latest",
          "--read-only",
          "--project-ref=<project-ref>",
        ],
        "env": {
          "SUPABASE_ACCESS_TOKEN": "<personal-access-token>",
        },
      },
    },
  },
}

```

to:
```json
{
  "context_servers": {
    "some-mcp-server": {
      "source": "custom",
      "command": "npx",
      "args": [
        "-y",
        "@supabase/mcp-server-supabase@latest",
        "--read-only",
        "--project-ref=<project-ref>",
      ],
      "env": {
        "SUPABASE_ACCESS_TOKEN": "<personal-access-token>",
      },
    },
  },
}
```


Which seems to be somewhat of a standard now (VSCode, Cursor, Windsurf,
...)

Release Notes:

- agent: Use standardised format for configuring MCP Servers

crates/agent_ui/src/agent_configuration/configure_context_server_modal.rs

@@ -180,7 +180,7 @@ impl ConfigurationSource {
 }
 
 fn context_server_input(existing: Option<(ContextServerId, ContextServerCommand)>) -> String {
-    let (name, path, args, env) = match existing {
+    let (name, command, args, env) = match existing {
         Some((id, cmd)) => {
             let args = serde_json::to_string(&cmd.args).unwrap();
             let env = serde_json::to_string(&cmd.env.unwrap_or_default()).unwrap();
@@ -198,14 +198,12 @@ fn context_server_input(existing: Option<(ContextServerId, ContextServerCommand)
         r#"{{
   /// The name of your MCP server
   "{name}": {{
-    "command": {{
-      /// The path to the executable
-      "path": "{path}",
-      /// The arguments to pass to the executable
-      "args": {args},
-      /// The environment variables to set for the executable
-      "env": {env}
-    }}
+    /// The command which runs the MCP server
+    "command": "{command}",
+    /// The arguments to pass to the MCP server
+    "args": {args},
+    /// The environment variables to set
+    "env": {env}
   }}
 }}"#
     )
@@ -439,8 +437,7 @@ fn parse_input(text: &str) -> Result<(ContextServerId, ContextServerCommand)> {
     let object = value.as_object().context("Expected object")?;
     anyhow::ensure!(object.len() == 1, "Expected exactly one key-value pair");
     let (context_server_name, value) = object.into_iter().next().unwrap();
-    let command = value.get("command").context("Expected command")?;
-    let command: ContextServerCommand = serde_json::from_value(command.clone())?;
+    let command: ContextServerCommand = serde_json::from_value(value.clone())?;
     Ok((ContextServerId(context_server_name.clone().into()), command))
 }
 

crates/context_server/src/context_server.rs

@@ -29,6 +29,7 @@ impl Display for ContextServerId {
 
 #[derive(Deserialize, Serialize, Clone, PartialEq, Eq, JsonSchema)]
 pub struct ContextServerCommand {
+    #[serde(rename = "command")]
     pub path: String,
     pub args: Vec<String>,
     pub env: Option<HashMap<String, String>>,

crates/migrator/src/migrations.rs

@@ -87,3 +87,9 @@ pub(crate) mod m_2025_06_25 {
 
     pub(crate) use settings::SETTINGS_PATTERNS;
 }
+
+pub(crate) mod m_2025_06_27 {
+    mod settings;
+
+    pub(crate) use settings::SETTINGS_PATTERNS;
+}

crates/migrator/src/migrations/m_2025_06_27/settings.rs

@@ -0,0 +1,133 @@
+use std::ops::Range;
+use tree_sitter::{Query, QueryMatch};
+
+use crate::MigrationPatterns;
+
+pub const SETTINGS_PATTERNS: MigrationPatterns = &[(
+    SETTINGS_CONTEXT_SERVER_PATTERN,
+    flatten_context_server_command,
+)];
+
+const SETTINGS_CONTEXT_SERVER_PATTERN: &str = r#"(document
+    (object
+        (pair
+            key: (string (string_content) @context-servers)
+            value: (object
+                (pair
+                    key: (string (string_content) @server-name)
+                    value: (object
+                        (pair
+                            key: (string (string_content) @source-key)
+                            value: (string (string_content) @source-value)
+                        )
+                        (pair
+                            key: (string (string_content) @command-key)
+                            value: (object) @command-object
+                        ) @command-pair
+                    ) @server-settings
+                )
+            )
+        )
+    )
+    (#eq? @context-servers "context_servers")
+    (#eq? @source-key "source")
+    (#eq? @source-value "custom")
+    (#eq? @command-key "command")
+)"#;
+
+fn flatten_context_server_command(
+    contents: &str,
+    mat: &QueryMatch,
+    query: &Query,
+) -> Option<(Range<usize>, String)> {
+    let command_pair_index = query.capture_index_for_name("command-pair")?;
+    let command_pair = mat.nodes_for_capture_index(command_pair_index).next()?;
+
+    let command_object_index = query.capture_index_for_name("command-object")?;
+    let command_object = mat.nodes_for_capture_index(command_object_index).next()?;
+
+    let server_settings_index = query.capture_index_for_name("server-settings")?;
+    let _server_settings = mat.nodes_for_capture_index(server_settings_index).next()?;
+
+    // Parse the command object to extract path, args, and env
+    let mut path_value = None;
+    let mut args_value = None;
+    let mut env_value = None;
+
+    let mut cursor = command_object.walk();
+    for child in command_object.children(&mut cursor) {
+        if child.kind() == "pair" {
+            if let Some(key_node) = child.child_by_field_name("key") {
+                if let Some(string_content) = key_node.child(1) {
+                    let key = &contents[string_content.byte_range()];
+                    if let Some(value_node) = child.child_by_field_name("value") {
+                        let value_range = value_node.byte_range();
+                        match key {
+                            "path" => path_value = Some(&contents[value_range]),
+                            "args" => args_value = Some(&contents[value_range]),
+                            "env" => env_value = Some(&contents[value_range]),
+                            _ => {}
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+    let path = path_value?;
+
+    // Get the proper indentation from the command pair
+    let command_pair_start = command_pair.start_byte();
+    let line_start = contents[..command_pair_start]
+        .rfind('\n')
+        .map(|pos| pos + 1)
+        .unwrap_or(0);
+    let indent = &contents[line_start..command_pair_start];
+
+    // Build the replacement string
+    let mut replacement = format!("\"command\": {}", path);
+
+    // Add args if present - need to reduce indentation
+    if let Some(args) = args_value {
+        replacement.push_str(",\n");
+        replacement.push_str(indent);
+        replacement.push_str("\"args\": ");
+        let reduced_args = reduce_indentation(args, 4);
+        replacement.push_str(&reduced_args);
+    }
+
+    // Add env if present - need to reduce indentation
+    if let Some(env) = env_value {
+        replacement.push_str(",\n");
+        replacement.push_str(indent);
+        replacement.push_str("\"env\": ");
+        replacement.push_str(&reduce_indentation(env, 4));
+    }
+
+    let range_to_replace = command_pair.byte_range();
+    Some((range_to_replace, replacement))
+}
+
+fn reduce_indentation(text: &str, spaces: usize) -> String {
+    let lines: Vec<&str> = text.lines().collect();
+    let mut result = String::new();
+
+    for (i, line) in lines.iter().enumerate() {
+        if i > 0 {
+            result.push('\n');
+        }
+
+        // Count leading spaces
+        let leading_spaces = line.chars().take_while(|&c| c == ' ').count();
+
+        if leading_spaces >= spaces {
+            // Reduce indentation
+            result.push_str(&line[spaces..]);
+        } else {
+            // Keep line as is if it doesn't have enough indentation
+            result.push_str(line);
+        }
+    }
+
+    result
+}

crates/migrator/src/migrator.rs

@@ -156,6 +156,10 @@ pub fn migrate_settings(text: &str) -> Result<Option<String>> {
             migrations::m_2025_06_25::SETTINGS_PATTERNS,
             &SETTINGS_QUERY_2025_06_25,
         ),
+        (
+            migrations::m_2025_06_27::SETTINGS_PATTERNS,
+            &SETTINGS_QUERY_2025_06_27,
+        ),
     ];
     run_migrations(text, migrations)
 }
@@ -262,6 +266,10 @@ define_query!(
     SETTINGS_QUERY_2025_06_25,
     migrations::m_2025_06_25::SETTINGS_PATTERNS
 );
+define_query!(
+    SETTINGS_QUERY_2025_06_27,
+    migrations::m_2025_06_27::SETTINGS_PATTERNS
+);
 
 // custom query
 static EDIT_PREDICTION_SETTINGS_MIGRATION_QUERY: LazyLock<Query> = LazyLock::new(|| {
@@ -286,6 +294,15 @@ mod tests {
         pretty_assertions::assert_eq!(migrated.as_deref(), output);
     }
 
+    fn assert_migrate_settings_with_migrations(
+        migrations: &[(MigrationPatterns, &Query)],
+        input: &str,
+        output: Option<&str>,
+    ) {
+        let migrated = run_migrations(input, migrations).unwrap();
+        pretty_assertions::assert_eq!(migrated.as_deref(), output);
+    }
+
     #[test]
     fn test_replace_array_with_single_string() {
         assert_migrate_keymap(
@@ -873,7 +890,11 @@ mod tests {
 
     #[test]
     fn test_mcp_settings_migration() {
-        assert_migrate_settings(
+        assert_migrate_settings_with_migrations(
+            &[(
+                migrations::m_2025_06_16::SETTINGS_PATTERNS,
+                &SETTINGS_QUERY_2025_06_16,
+            )],
             r#"{
     "context_servers": {
         "empty_server": {},
@@ -1058,7 +1079,14 @@ mod tests {
         }
     }
 }"#;
-        assert_migrate_settings(settings, None);
+        assert_migrate_settings_with_migrations(
+            &[(
+                migrations::m_2025_06_16::SETTINGS_PATTERNS,
+                &SETTINGS_QUERY_2025_06_16,
+            )],
+            settings,
+            None,
+        );
     }
 
     #[test]
@@ -1131,4 +1159,100 @@ mod tests {
             None,
         );
     }
+
+    #[test]
+    fn test_flatten_context_server_command() {
+        assert_migrate_settings(
+            r#"{
+    "context_servers": {
+        "some-mcp-server": {
+            "source": "custom",
+            "command": {
+                "path": "npx",
+                "args": [
+                    "-y",
+                    "@supabase/mcp-server-supabase@latest",
+                    "--read-only",
+                    "--project-ref=<project-ref>"
+                ],
+                "env": {
+                    "SUPABASE_ACCESS_TOKEN": "<personal-access-token>"
+                }
+            }
+        }
+    }
+}"#,
+            Some(
+                r#"{
+    "context_servers": {
+        "some-mcp-server": {
+            "source": "custom",
+            "command": "npx",
+            "args": [
+                "-y",
+                "@supabase/mcp-server-supabase@latest",
+                "--read-only",
+                "--project-ref=<project-ref>"
+            ],
+            "env": {
+                "SUPABASE_ACCESS_TOKEN": "<personal-access-token>"
+            }
+        }
+    }
+}"#,
+            ),
+        );
+
+        // Test with additional keys in server object
+        assert_migrate_settings(
+            r#"{
+    "context_servers": {
+        "server-with-extras": {
+            "source": "custom",
+            "command": {
+                "path": "/usr/bin/node",
+                "args": ["server.js"]
+            },
+            "settings": {}
+        }
+    }
+}"#,
+            Some(
+                r#"{
+    "context_servers": {
+        "server-with-extras": {
+            "source": "custom",
+            "command": "/usr/bin/node",
+            "args": ["server.js"],
+            "settings": {}
+        }
+    }
+}"#,
+            ),
+        );
+
+        // Test command without args or env
+        assert_migrate_settings(
+            r#"{
+    "context_servers": {
+        "simple-server": {
+            "source": "custom",
+            "command": {
+                "path": "simple-mcp-server"
+            }
+        }
+    }
+}"#,
+            Some(
+                r#"{
+    "context_servers": {
+        "simple-server": {
+            "source": "custom",
+            "command": "simple-mcp-server"
+        }
+    }
+}"#,
+            ),
+        );
+    }
 }

crates/project/src/project_settings.rs

@@ -97,9 +97,8 @@ pub enum ContextServerSettings {
         /// Whether the context server is enabled.
         #[serde(default = "default_true")]
         enabled: bool,
-        /// The command to run this context server.
-        ///
-        /// This will override the command set by an extension.
+
+        #[serde(flatten)]
         command: ContextServerCommand,
     },
     Extension {