fix: update git hooks and package manager consistency

.husky/commit-msg

@@ -1,2 +1,2 @@
 # Validate commit message with commitlint
-# npx --no -- commitlint --edit $1
+pnpm exec commitlint --edit $1

CHANGELOG.md

@@ -1,37 +1,32 @@
 ## [0.10.1](https://github.com/drivecore/mycoder/compare/v0.10.0...v0.10.1) (2025-03-11)
 
-
 ### Bug Fixes
 
-* token caching ([5972e59](https://github.com/drivecore/mycoder/commit/5972e59ab572040e564d1756ab8a5625215e14dc))
+- token caching ([5972e59](https://github.com/drivecore/mycoder/commit/5972e59ab572040e564d1756ab8a5625215e14dc))
 
 # [0.10.0](https://github.com/drivecore/mycoder/compare/v0.9.0...v0.10.0) (2025-03-11)
 
-
 ### Bug Fixes
 
-* add deepmerge to cli package.json ([ab66377](https://github.com/drivecore/mycoder/commit/ab66377342c9f23fa874d2776e73d365141e8801))
-* update hierarchical configuration system to fix failing tests ([93d949c](https://github.com/drivecore/mycoder/commit/93d949c03b7ebe96bad36713f6476c38d2a35224))
-
+- add deepmerge to cli package.json ([ab66377](https://github.com/drivecore/mycoder/commit/ab66377342c9f23fa874d2776e73d365141e8801))
+- update hierarchical configuration system to fix failing tests ([93d949c](https://github.com/drivecore/mycoder/commit/93d949c03b7ebe96bad36713f6476c38d2a35224))
 
 ### Features
 
-* add back token tracking, system prompt caching. ([ddc04ab](https://github.com/drivecore/mycoder/commit/ddc04ab0778eb2f571897e825c8d8ba17651db09))
-* add showStdIn and showStdout options to shellMessage and shellStart ([aed1b9f](https://github.com/drivecore/mycoder/commit/aed1b9f6ba489da19f2170c136861a7c80ad6e33)), closes [#167](https://github.com/drivecore/mycoder/issues/167)
-* add token caching.  issue 145 ([d78723b](https://github.com/drivecore/mycoder/commit/d78723bb6d0514110088caf7009e196e3f79769e))
-* implement hierarchical configuration system ([84d73d1](https://github.com/drivecore/mycoder/commit/84d73d1e6324670890a203f455fe257aeb6ed07a)), closes [#153](https://github.com/drivecore/mycoder/issues/153)
+- add back token tracking, system prompt caching. ([ddc04ab](https://github.com/drivecore/mycoder/commit/ddc04ab0778eb2f571897e825c8d8ba17651db09))
+- add showStdIn and showStdout options to shellMessage and shellStart ([aed1b9f](https://github.com/drivecore/mycoder/commit/aed1b9f6ba489da19f2170c136861a7c80ad6e33)), closes [#167](https://github.com/drivecore/mycoder/issues/167)
+- add token caching. issue 145 ([d78723b](https://github.com/drivecore/mycoder/commit/d78723bb6d0514110088caf7009e196e3f79769e))
+- implement hierarchical configuration system ([84d73d1](https://github.com/drivecore/mycoder/commit/84d73d1e6324670890a203f455fe257aeb6ed07a)), closes [#153](https://github.com/drivecore/mycoder/issues/153)
 
 # [0.9.0](https://github.com/drivecore/mycoder/compare/v0.8.0...v0.9.0) (2025-03-11)
 
-
 ### Bug Fixes
 
-* don't save consent when using --userWarning=false ([41cf69d](https://github.com/drivecore/mycoder/commit/41cf69dee22acc31cd0f2aa9f80e36cd867fb20b))
-
+- don't save consent when using --userWarning=false ([41cf69d](https://github.com/drivecore/mycoder/commit/41cf69dee22acc31cd0f2aa9f80e36cd867fb20b))
 
 ### Features
 
-* add CLI options for automated usage scenarios ([00419bc](https://github.com/drivecore/mycoder/commit/00419bc3e060db6d0c18fc72e2d7b6957791c875))
+- add CLI options for automated usage scenarios ([00419bc](https://github.com/drivecore/mycoder/commit/00419bc3e060db6d0c18fc72e2d7b6957791c875))
 
 # [0.8.0](https://github.com/drivecore/mycoder/compare/v0.7.0...v0.8.0) (2025-03-11)
 

docs/release-process.md

@@ -1 +1 @@
-# Release Process with semantic-release-monorepo\n\n## Overview\n\nThis project uses `semantic-release-monorepo` to automate the versioning and release process across all packages in the monorepo. This ensures that each package is versioned independently based on its own changes, while maintaining a consistent release process.\n\n## How It Works\n\n1. When code is pushed to the `release` branch, the GitHub Actions workflow is triggered.\n2. The workflow builds and tests all packages.\n3. `semantic-release-monorepo` analyzes the commit history for each package to determine the next version.\n4. New versions are published to npm, and release notes are generated based on conventional commits.\n5. Git tags are created for each package release.\n\n## Commit Message Format\n\nThis project follows the [Conventional Commits](https://www.conventionalcommits.org/) specification. Your commit messages should be structured as follows:\n\n```\n<type>[optional scope]: <description>\n\n[optional body]\n\n[optional footer(s)]\n```\n\nExamples:\n\n```\nfeat(cli): add new command for project initialization\nfix(agent): resolve issue with async tool execution\ndocs: update installation instructions\n```\n\n### Types\n\n- `feat`: A new feature (triggers a minor version bump)\n- `fix`: A bug fix (triggers a patch version bump)\n- `docs`: Documentation changes\n- `style`: Changes that don't affect the code's meaning (formatting, etc.)\n- `refactor`: Code changes that neither fix a bug nor add a feature\n- `perf`: Performance improvements\n- `test`: Adding or correcting tests\n- `chore`: Changes to the build process, tooling, etc.\n\n### Breaking Changes\n\nIf your commit introduces a breaking change, add `BREAKING CHANGE:` in the footer followed by a description of the change. This will trigger a major version bump.\n\nExample:\n\n```\nfeat(agent): change API for tool execution\n\nBREAKING CHANGE: The tool execution API now requires an options object instead of individual parameters.\n```\n\n## Troubleshooting\n\nIf you encounter issues with the release process:\n\n1. Run `pnpm verify-release-config` to check if your semantic-release configuration is correct.\n2. Ensure your commit messages follow the conventional commits format.\n3. Check if the package has a `.releaserc.json` file that extends `semantic-release-monorepo`.\n4. Verify that each package has a `semantic-release` script in its `package.json`.\n\n## Manual Release\n\nIn rare cases, you might need to trigger a release manually. You can do this by:\n\n```bash\n# Release all packages\npnpm release\n\n# Release a specific package\ncd packages/cli\npnpm semantic-release\n```\n
+# Release Process with semantic-release-monorepo\n\n## Overview\n\nThis project uses `semantic-release-monorepo` to automate the versioning and release process across all packages in the monorepo. This ensures that each package is versioned independently based on its own changes, while maintaining a consistent release process.\n\n## How It Works\n\n1. When code is pushed to the `release` branch, the GitHub Actions workflow is triggered.\n2. The workflow builds and tests all packages.\n3. `semantic-release-monorepo` analyzes the commit history for each package to determine the next version.\n4. New versions are published to npm, and release notes are generated based on conventional commits.\n5. Git tags are created for each package release.\n\n## Commit Message Format\n\nThis project follows the [Conventional Commits](https://www.conventionalcommits.org/) specification. Your commit messages should be structured as follows:\n\n`\n<type>[optional scope]: <description>\n\n[optional body]\n\n[optional footer(s)]\n`\n\nExamples:\n\n`\nfeat(cli): add new command for project initialization\nfix(agent): resolve issue with async tool execution\ndocs: update installation instructions\n`\n\n### Types\n\n- `feat`: A new feature (triggers a minor version bump)\n- `fix`: A bug fix (triggers a patch version bump)\n- `docs`: Documentation changes\n- `style`: Changes that don't affect the code's meaning (formatting, etc.)\n- `refactor`: Code changes that neither fix a bug nor add a feature\n- `perf`: Performance improvements\n- `test`: Adding or correcting tests\n- `chore`: Changes to the build process, tooling, etc.\n\n### Breaking Changes\n\nIf your commit introduces a breaking change, add `BREAKING CHANGE:` in the footer followed by a description of the change. This will trigger a major version bump.\n\nExample:\n\n`\nfeat(agent): change API for tool execution\n\nBREAKING CHANGE: The tool execution API now requires an options object instead of individual parameters.\n`\n\n## Troubleshooting\n\nIf you encounter issues with the release process:\n\n1. Run `pnpm verify-release-config` to check if your semantic-release configuration is correct.\n2. Ensure your commit messages follow the conventional commits format.\n3. Check if the package has a `.releaserc.json` file that extends `semantic-release-monorepo`.\n4. Verify that each package has a `semantic-release` script in its `package.json`.\n\n## Manual Release\n\nIn rare cases, you might need to trigger a release manually. You can do this by:\n\n`bash\n# Release all packages\npnpm release\n\n# Release a specific package\ncd packages/cli\npnpm semantic-release\n`\n

eslint.config.js

@@ -75,6 +75,7 @@ export default ts.config(
       '**/.output',
       '**/pnpm-lock.yaml',
       '**/routeTree.gen.ts',
+      'scripts/verify-release-config.js',
     ],
   },
 );

lerna.json

@@ -1 +1,11 @@
-{\n  \"version\": \"independent\",\n  \"npmClient\": \"pnpm\",\n  \"command\": {\n    \"publish\": {\n      \"conventionalCommits\": true,\n      \"message\": \"chore(release): publish\"\n    }\n  },\n  \"packages\": [\"packages/*\"]\n}
+{
+  "version": "independent",
+  "npmClient": "pnpm",
+  "command": {
+    "publish": {
+      "conventionalCommits": true,
+      "message": "chore(release): publish"
+    }
+  },
+  "packages": ["packages/*"]
+}

lerna.json.bak

@@ -0,0 +1 @@
+{\n  \"version\": \"independent\",\n  \"npmClient\": \"pnpm\",\n  \"command\": {\n    \"publish\": {\n      \"conventionalCommits\": true,\n      \"message\": \"chore(release): publish\"\n    }\n  },\n  \"packages\": [\"packages/*\"]\n}

package.json

@@ -17,13 +17,13 @@
     "format": "prettier . --write",
     "clean": "pnpm -r clean",
     "clean:all": "pnpm -r clean:all && rimraf node_modules",
-    "cloc": "npx cloc * --exclude-dir=node_modules,dist,.vinxi,.output",
+    "cloc": "pnpm exec cloc * --exclude-dir=node_modules,dist,.vinxi,.output",
     "gcloud-setup": "gcloud auth application-default login && gcloud config set account \"ben@drivecore.ai\" && gcloud config set project drivecore-primary && gcloud config set run/region us-central1",
     "cli": "cd packages/cli && node --no-deprecation bin/cli.js",
     "prepare": "husky",
     "semantic-release": "semantic-release",
     "verify-release-config": "node scripts/verify-release-config.js",
-    "release": "pnpm verify-release-config && npx lerna exec --concurrency 1 -- npx --no-install semantic-release -e semantic-release-monorepo"
+    "release": "pnpm verify-release-config && pnpm exec lerna exec --concurrency 1 -- pnpm exec semantic-release -e semantic-release-monorepo"
   },
   "lint-staged": {
     "*.{js,jsx,ts,tsx}": [

packages/agent/src/index.ts

@@ -25,7 +25,13 @@ export * from './tools/interaction/userPrompt.js';
 // Core
 export * from './core/executeToolCall.js';
 export * from './core/types.js';
-export * from './core/toolAgent/index.js';
+// Tool Agent Core
+export { toolAgent } from './core/toolAgent/toolAgentCore.js';
+export * from './core/toolAgent/config.js';
+export * from './core/toolAgent/messageUtils.js';
+export * from './core/toolAgent/toolExecutor.js';
+export * from './core/toolAgent/tokenTracking.js';
+export * from './core/toolAgent/types.js';
 
 // Utils
 export * from './tools/getTools.js';

packages/agent/src/tools/interaction/subAgent.ts

@@ -4,8 +4,8 @@ import { zodToJsonSchema } from 'zod-to-json-schema';
 import {
   getDefaultSystemPrompt,
   getModel,
-  toolAgent,
-} from '../../core/toolAgent/index.js';
+} from '../../core/toolAgent/config.js';
+import { toolAgent } from '../../core/toolAgent/toolAgentCore.js';
 import { Tool, ToolContext } from '../../core/types.js';
 import { getTools } from '../getTools.js';
 

packages/agent/src/utils/logger.test.ts

@@ -9,7 +9,7 @@ describe('Logger', () => {
     // Setup console spies before each test
     consoleSpy = {
       log: vi.spyOn(console, 'log').mockImplementation(() => {}),
-      info: vi.spyOn(console, 'log').mockImplementation(() => {}),
+      info: vi.spyOn(console, 'info').mockImplementation(() => {}),
       warn: vi.spyOn(console, 'warn').mockImplementation(() => {}),
       error: vi.spyOn(console, 'error').mockImplementation(() => {}),
     };

packages/agent/src/utils/logger.ts

@@ -34,7 +34,11 @@ export const BasicLoggerStyler = {
   ): string =>
     level === LogLevel.debug || level === LogLevel.verbose
       ? chalk.dim(prefix)
-      : '',
+      : prefix,
+  showPrefix: (_level: LogLevel): boolean => {
+    // Show prefix for all log levels
+    return true;
+  },
 };
 
 const loggerStyle = BasicLoggerStyler;
@@ -93,17 +97,21 @@ export class Logger {
   private formatMessages(level: LogLevel, messages: unknown[]): string {
     const formatted = this.toStrings(messages);
     const messageColor = loggerStyle.getColor(level, this.nesting);
-    const prefix = loggerStyle.formatPrefix(
-      `[${this.name}]`,
-      level,
-      this.nesting,
-    );
-
-    let combinedPrefix = `${this.prefix}${prefix}`;
-    if (this.customPrefix) {
-      combinedPrefix = `${this.prefix}${this.customPrefix} `;
-    } else if (combinedPrefix.length > 0) {
-      combinedPrefix += ' ';
+
+    let combinedPrefix = this.prefix;
+
+    if (loggerStyle.showPrefix(level)) {
+      const prefix = loggerStyle.formatPrefix(
+        `[${this.name}]`,
+        level,
+        this.nesting,
+      );
+
+      if (this.customPrefix) {
+        combinedPrefix = `${this.prefix}${this.customPrefix} `;
+      } else {
+        combinedPrefix = `${this.prefix}${prefix} `;
+      }
     }
 
     return formatted
@@ -113,27 +121,27 @@ export class Logger {
   }
 
   log(level: LogLevel, ...messages: unknown[]): void {
-    if (this.logLevelIndex > level) return;
+    if (level < this.logLevelIndex) return;
     console.log(this.formatMessages(level, messages));
   }
 
   debug(...messages: unknown[]): void {
-    if (this.logLevelIndex > LogLevel.debug) return;
+    if (LogLevel.debug < this.logLevelIndex) return;
     console.log(this.formatMessages(LogLevel.debug, messages));
   }
 
   verbose(...messages: unknown[]): void {
-    if (this.logLevelIndex > LogLevel.verbose) return;
+    if (LogLevel.verbose < this.logLevelIndex) return;
     console.log(this.formatMessages(LogLevel.verbose, messages));
   }
 
   info(...messages: unknown[]): void {
-    if (this.logLevelIndex > LogLevel.info) return;
+    if (LogLevel.info < this.logLevelIndex) return;
     console.log(this.formatMessages(LogLevel.info, messages));
   }
 
   warn(...messages: unknown[]): void {
-    if (this.logLevelIndex > LogLevel.warn) return;
+    if (LogLevel.warn < this.logLevelIndex) return;
     console.warn(this.formatMessages(LogLevel.warn, messages));
   }
 

packages/cli/src/commands/config.ts

@@ -1,5 +1,3 @@
-import { createInterface } from 'readline/promises';
-
 import chalk from 'chalk';
 import { Logger } from 'mycoder-agent';
 
@@ -14,25 +12,6 @@ import {
 } from '../settings/config.js';
 import { nameToLogIndex } from '../utils/nameToLogIndex.js';
 
-/**
- * Prompts the user for confirmation with a yes/no question
- * @param question The question to ask the user
- * @returns True if the user confirmed, false otherwise
- */
-async function confirm(question: string): Promise<boolean> {
-  const rl = createInterface({
-    input: process.stdin,
-    output: process.stdout,
-  });
-
-  try {
-    const answer = await rl.question(`${question} (y/N): `);
-    return answer.toLowerCase() === 'y' || answer.toLowerCase() === 'yes';
-  } finally {
-    rl.close();
-  }
-}
-
 import type { CommandModule, ArgumentsCamelCase } from 'yargs';
 
 export interface ConfigOptions extends SharedOptions {
@@ -200,30 +179,6 @@ export const command: CommandModule<SharedOptions, ConfigOptions> = {
         // Continue with the operation instead of returning
       }
 
-      // Check if this is an API key and add a warning
-      if (argv.key.includes('API_KEY')) {
-        logger.warn(
-          chalk.yellow(
-            'Warning: Storing API keys in configuration is less secure than using environment variables.',
-          ),
-        );
-        logger.warn(
-          chalk.yellow(
-            'Your API key will be stored in plaintext in the configuration file.',
-          ),
-        );
-
-        // Ask for confirmation
-        const isConfirmed = await confirm(
-          'Do you want to continue storing your API key in the configuration?',
-        );
-
-        if (!isConfirmed) {
-          logger.info('Operation cancelled.');
-          return;
-        }
-      }
-
       // Parse the value based on current type or infer boolean/number
       let parsedValue: string | boolean | number = argv.value;
 
@@ -277,16 +232,6 @@ export const command: CommandModule<SharedOptions, ConfigOptions> = {
     if (argv.command === 'clear') {
       // Check if --all flag is provided
       if (argv.all) {
-        // Confirm with the user before clearing all settings
-        const isConfirmed = await confirm(
-          'Are you sure you want to clear all configuration settings? This action cannot be undone.',
-        );
-
-        if (!isConfirmed) {
-          logger.info('Operation cancelled.');
-          return;
-        }
-
         try {
           // Clear settings at the specified level
           clearConfigAtLevel(configLevel);

packages/cli/src/settings/settings.ts

@@ -18,17 +18,20 @@ export const getSettingsDir = (): string => {
 export const getProjectSettingsDir = (): string => {
   // Start with the current directory
   let currentDir = process.cwd();
-  
+
   // Traverse up the directory tree until we find a .mycoder directory or reach the root
   while (currentDir !== path.parse(currentDir).root) {
     const projectSettingsDir = path.join(currentDir, '.mycoder');
-    if (fs.existsSync(projectSettingsDir) && fs.statSync(projectSettingsDir).isDirectory()) {
+    if (
+      fs.existsSync(projectSettingsDir) &&
+      fs.statSync(projectSettingsDir).isDirectory()
+    ) {
       return projectSettingsDir;
     }
     // Move up one directory
     currentDir = path.dirname(currentDir);
   }
-  
+
   // If we're creating a new project config, use the current directory
   return path.join(process.cwd(), '.mycoder');
 };
@@ -39,7 +42,7 @@ export const getProjectSettingsDir = (): string => {
  */
 export const isProjectSettingsDirWritable = (): boolean => {
   const projectDir = getProjectSettingsDir();
-  
+
   // Check if directory exists
   if (fs.existsSync(projectDir)) {
     try {