feat(config): make assistants configuration project-scoped

src/cli/commands/assistants/constants.ts

@@ -79,6 +79,11 @@ export const MESSAGES = {
     SUMMARY_REGISTERED: (count: number) => `  Registered: ${count}`,
     SUMMARY_UNREGISTERED: (count: number) => `  Unregistered: ${count}`,
     SUMMARY_PROFILE: (profile: string) => `  Profile: ${profile}\n`,
-    CURRENTLY_REGISTERED: 'Currently registered assistants:'
+    CURRENTLY_REGISTERED: 'Currently registered assistants:',
+    PROMPT_STORAGE_SCOPE: 'Where would you like to save assistant configuration?',
+    STORAGE_GLOBAL_LABEL: 'Global (~/.codemie/) - Available across all projects',
+    STORAGE_LOCAL_LABEL: 'Local (.codemie/) - Only for this project',
+    STORAGE_LOCAL_NOTE: 'Project-scoped assistants will override global ones for this repository.',
+    SUMMARY_CONFIG_LOCATION: (location: string) => `  Config: ${location}\n`
   }
 } as const;

src/cli/commands/assistants/setup/index.ts

@@ -84,6 +84,108 @@ function handleError(error: unknown): never {
   process.exit(1);
 }
 
+/**
+ * Prompt user to choose where to save assistant configuration.
+ * Implemented as a raw-mode TUI (same as promptModeSelection) to avoid
+ * stdin state issues after the custom TUI prompts that precede it.
+ */
+async function promptStorageScope(): Promise<'global' | 'local'> {
+  const ANSI = {
+    CLEAR_SCREEN: '\x1B[2J\x1B[H',
+    HIDE_CURSOR: '\x1B[?25l',
+    SHOW_CURSOR: '\x1B[?25h',
+  } as const;
+
+  const KEY = {
+    UP: '\x1B[A',
+    DOWN: '\x1B[B',
+    ENTER: '\r',
+    ESC: '\x1B',
+    CTRL_C: '\x03',
+  } as const;
+
+  const choices = ['global', 'local'] as const;
+  let selectedIndex = 0;
+
+  function renderUI(): string {
+    const lines: string[] = [
+      '',
+      `  ${MESSAGES.SETUP.PROMPT_STORAGE_SCOPE}`,
+      '',
+    ];
+
+    choices.forEach((choice, i) => {
+      const marker = i === selectedIndex ? chalk.cyan('●') : chalk.dim('○');
+      const label = choice === 'global'
+        ? `${chalk.cyan('Global')} ${chalk.dim(MESSAGES.SETUP.STORAGE_GLOBAL_LABEL)}`
+        : `${chalk.yellow('Local')} ${chalk.dim(MESSAGES.SETUP.STORAGE_LOCAL_LABEL)}`;
+      lines.push(`  ${marker} ${label}`);
+    });
+
+    lines.push('');
+    lines.push(chalk.dim('  ↑↓ Navigate   Enter Confirm'));
+
+    if (selectedIndex === 1) {
+      lines.push('');
+      lines.push(chalk.dim(`  ${MESSAGES.SETUP.STORAGE_LOCAL_NOTE}`));
+    }
+
+    lines.push('');
+    return lines.join('\n');
+  }
+
+  return new Promise((resolve) => {
+    let keepAliveTimer: NodeJS.Timeout | null = null;
+
+    function cleanup() {
+      if (keepAliveTimer) {
+        clearInterval(keepAliveTimer);
+        keepAliveTimer = null;
+      }
+      process.stdin.setRawMode(false);
+      process.stdin.pause();
+      process.stdin.removeAllListeners('data');
+      process.stdout.write(ANSI.SHOW_CURSOR + ANSI.CLEAR_SCREEN);
+    }
+
+    function stop(choice: 'global' | 'local') {
+      cleanup();
+      resolve(choice);
+    }
+
+    function render() {
+      process.stdout.write(ANSI.CLEAR_SCREEN + ANSI.HIDE_CURSOR + renderUI());
+    }
+
+    process.stdin.setRawMode(true);
+    process.stdin.resume();
+    process.stdin.setEncoding('utf8');
+
+    process.stdin.on('data', (key: string) => {
+      switch (key) {
+        case KEY.UP:
+          selectedIndex = Math.max(0, selectedIndex - 1);
+          render();
+          break;
+        case KEY.DOWN:
+          selectedIndex = Math.min(choices.length - 1, selectedIndex + 1);
+          render();
+          break;
+        case KEY.ENTER:
+          stop(choices[selectedIndex]);
+          break;
+        case KEY.ESC:
+        case KEY.CTRL_C:
+          stop('global');
+          break;
+      }
+    });
+
+    keepAliveTimer = setInterval(() => {}, 60000);
+    render();
+  });
+}
+
 /**
  * Setup assistants - unified list/register/unregister
  */
@@ -165,6 +267,9 @@ async function setupAssistants(options: SetupCommandOptions): Promise<void> {
     }
   }
 
+  // Prompt for storage scope before making any changes
+  const storageScope = await promptStorageScope();
+
   // Apply changes and get summary data
   const { newRegistrations, registered, unregistered } = await applyChanges(
     selectedIds,
@@ -173,12 +278,29 @@ async function setupAssistants(options: SetupCommandOptions): Promise<void> {
     registrationModes
   );
 
-  // Update config
+  // Always reflect new state in config for display purposes
   config.codemieAssistants = newRegistrations;
-  await ConfigLoader.saveProfile(profileName, config);
+
+  // Skip saving (and showing configLocation) when nothing changed
+  if (registered.length === 0 && unregistered.length === 0) {
+    displaySummary(registered, unregistered, profileName, config);
+    return;
+  }
+
+  // Save to the appropriate config location
+  const workingDir = process.cwd();
+  let configLocation: string;
+
+  if (storageScope === 'local') {
+    await ConfigLoader.saveAssistantsToProjectConfig(workingDir, profileName, newRegistrations);
+    configLocation = `${workingDir}/.codemie/codemie-cli.config.json`;
+  } else {
+    await ConfigLoader.saveProfile(profileName, config);
+    configLocation = `global (~/.codemie/codemie-cli.config.json)`;
+  }
 
   // Display summary
-  displaySummary(registered, unregistered, profileName, config);
+  displaySummary(registered, unregistered, profileName, config, configLocation);
 }
 
 /**

src/cli/commands/assistants/setup/summary/index.ts

@@ -18,11 +18,15 @@ export function displaySummary(
   toRegister: Assistant[],
   toUnregister: CodemieAssistant[],
   profileName: string,
-  config: ProviderProfile
+  config: ProviderProfile,
+  configLocation?: string
 ): void {
   const totalChanges = toRegister.length + toUnregister.length;
   console.log(chalk.green(MESSAGES.SETUP.SUMMARY_UPDATED(totalChanges)));
   console.log(chalk.dim(MESSAGES.SETUP.SUMMARY_PROFILE(profileName)));
+  if (configLocation) {
+    console.log(chalk.dim(MESSAGES.SETUP.SUMMARY_CONFIG_LOCATION(configLocation)));
+  }
 
   displayCurrentlyRegistered(config);
 }

src/utils/config.ts

@@ -659,6 +659,51 @@ export class ConfigLoader {
     );
   }
 
+  /**
+   * Save assistants configuration to project-local config file
+   * Only updates the codemieAssistants field in the specified profile,
+   * leaving all other local config fields untouched.
+   * Creates the local config file if it does not exist.
+   */
+  static async saveAssistantsToProjectConfig(
+    workingDir: string,
+    profileName: string,
+    assistants: CodemieAssistant[]
+  ): Promise<void> {
+    const localConfigPath = path.join(workingDir, this.LOCAL_CONFIG);
+    const configDir = path.dirname(localConfigPath);
+    await fs.mkdir(configDir, { recursive: true });
+
+    const rawConfig = await this.loadJsonConfig(localConfigPath);
+
+    let config: MultiProviderConfig;
+
+    if (isMultiProviderConfig(rawConfig)) {
+      config = rawConfig;
+    } else {
+      config = {
+        version: 2,
+        activeProfile: profileName,
+        profiles: {}
+      };
+    }
+
+    if (config.profiles[profileName]) {
+      config.profiles[profileName].codemieAssistants = assistants;
+    } else {
+      config.profiles[profileName] = { codemieAssistants: assistants };
+    }
+
+    // Keep activeProfile pointing at a valid profile.
+    // Update it to profileName when: no active profile is set, the current active
+    // profile no longer exists, or this is the only profile in the file.
+    if (!config.activeProfile || !config.profiles[config.activeProfile] || Object.keys(config.profiles).length === 1) {
+      config.activeProfile = profileName;
+    }
+
+    await fs.writeFile(localConfigPath, JSON.stringify(config, null, 2), 'utf-8');
+  }
+
   /**
    * Delete global config file
    */