chore: update dependencies and fix linting configuration

Author: prosdev

.changeset/config.json

@@ -8,4 +8,4 @@
   "baseBranch": "main",
   "updateInternalDependencies": "patch",
   "ignore": []
-}
+}

.husky/pre-commit

@@ -1,11 +1,2 @@
-# Get staged files
-files=$(git diff --cached --name-only --diff-filter=ACMR "*.ts" "*.tsx" "*.js" "*.jsx" | xargs)
-
-if [ -n "$files" ]; then
-  echo "Running Biome on staged files: $files"
-  pnpm lint-staged $files
-  git add $files
-fi
-
-# Run TypeScript type check
+pnpm lint-staged
 pnpm typecheck

biome.json

@@ -1,5 +1,5 @@
 {
-  "$schema": "https://biomejs.dev/schemas/2.3.0/schema.json",
+  "$schema": "https://biomejs.dev/schemas/2.3.8/schema.json",
   "assist": { "actions": { "source": { "organizeImports": "on" } } },
   "linter": {
     "enabled": true,
@@ -28,5 +28,10 @@
       "trailingCommas": "es5",
       "semicolons": "always"
     }
+  },
+  "vcs": {
+    "enabled": true,
+    "clientKind": "git",
+    "useIgnoreFile": true
   }
 }

commitlint.config.js

@@ -2,10 +2,6 @@ module.exports = {
   extends: ['@commitlint/config-conventional'],
   rules: {
     'body-max-line-length': [2, 'always', 100],
-    'subject-case': [
-      2,
-      'never',
-      ['start-case', 'pascal-case', 'upper-case'],
-    ],
+    'subject-case': [2, 'never', ['start-case', 'pascal-case', 'upper-case']],
   },
-};
+};

package.json

@@ -15,7 +15,18 @@
   "scripts": {
     "build": "pnpm -r build",
     "dev": "pnpm --filter @doc-agent/cli dev",
-    "mcp": "pnpm --filter @doc-agent/cli mcp"
+    "mcp": "pnpm --filter @doc-agent/cli mcp",
+    "lint": "biome check .",
+    "format": "biome format . --write",
+    "lint-staged": "lint-staged",
+    "check": "biome check .",
+    "typecheck": "tsc --noEmit",
+    "test": "vitest"
+  },
+  "lint-staged": {
+    "*.{js,ts,cjs,mjs,d.cts,d.mts,jsx,tsx,json,jsonc}": [
+      "biome check --write --no-errors-on-unmatched"
+    ]
   },
   "keywords": [
     "document",
@@ -32,7 +43,11 @@
     "packages/*"
   ],
   "devDependencies": {
+    "@biomejs/biome": "2.3.8",
     "@tsconfig/node-lts": "^24.0.0",
-    "typescript": "^5.9.3"
+    "@types/node": "^24.10.1",
+    "lint-staged": "16.2.7",
+    "typescript": "^5.9.3",
+    "vitest": "^4.0.15"
   }
-}
+}

packages/cli/package.json

@@ -18,16 +18,16 @@
     "@doc-agent/core": "workspace:*",
     "@doc-agent/extract": "workspace:*",
     "@doc-agent/vector-store": "workspace:*",
-    "@modelcontextprotocol/sdk": "^1.0.4",
-    "@google/generative-ai": "^0.21.0",
-    "vectordb": "^0.9.0",
-    "commander": "^12.1.0",
-    "ora": "^8.1.1",
-    "chalk": "^5.3.0"
+    "@google/generative-ai": "^0.24.1",
+    "@modelcontextprotocol/sdk": "^1.24.3",
+    "chalk": "^5.6.2",
+    "commander": "^14.0.2",
+    "ora": "^9.0.0",
+    "vectordb": "^0.21.2"
   },
   "devDependencies": {
-    "@types/node": "^20.17.9",
-    "typescript": "^5.7.2",
-    "tsx": "^4.19.2"
+    "@types/node": "^24.10.1",
+    "tsx": "^4.21.0",
+    "typescript": "^5.9.3"
   }
 }

packages/cli/src/cli.ts

@@ -1,11 +1,11 @@
 #!/usr/bin/env node
-import { Command } from 'commander';
-import ora from 'ora';
-import chalk from 'chalk';
-import { extractDocument } from '@doc-agent/extract';
-import type { Config } from '@doc-agent/core';
 import { exec } from 'node:child_process';
 import { promisify } from 'node:util';
+import type { Config } from '@doc-agent/core';
+import { extractDocument } from '@doc-agent/extract';
+import chalk from 'chalk';
+import { Command } from 'commander';
+import ora from 'ora';
 
 const execAsync = promisify(exec);
 
@@ -24,8 +24,8 @@ async function ensureOllamaModel(model: string) {
     if (!response.ok) {
       throw new Error('Ollama is not running. Please start Ollama first.');
     }
-    const data = await response.json() as { models: { name: string }[] };
-    const modelExists = data.models.some(m => m.name.includes(model));
+    const data = (await response.json()) as { models: { name: string }[] };
+    const modelExists = data.models.some((m) => m.name.includes(model));
 
     if (!modelExists) {
       spinner.text = `Pulling Ollama model: ${model} (this may take a while)...`;
@@ -46,31 +46,35 @@ program
   .command('extract <file>')
   .description('Extract structured data from a document')
   .option('-p, --provider <provider>', 'AI provider (gemini|openai|ollama)', 'ollama')
-  .option('-m, --model <model>', 'Model to use (default: llama3.2-vision for ollama)', 'llama3.2-vision')
+  .option(
+    '-m, --model <model>',
+    'Model to use (default: llama3.2-vision for ollama)',
+    'llama3.2-vision'
+  )
   .action(async (file: string, options) => {
     try {
       if (options.provider === 'ollama') {
         await ensureOllamaModel(options.model);
       }
 
       const spinner = ora('Extracting document data...').start();
-      
+
       const config: Config = {
         aiProvider: options.provider,
         geminiApiKey: process.env.GEMINI_API_KEY,
         openaiApiKey: process.env.OPENAI_API_KEY,
-        ollamaModel: options.model
+        ollamaModel: options.model,
       };
-      
+
       const result = await extractDocument(file, config);
-      
+
       spinner.succeed(chalk.green('Extraction complete!'));
       console.log(JSON.stringify(result, null, 2));
     } catch (error) {
       // Only fail the spinner if it's running (ensureOllamaModel might have failed already)
       if (ora().isSpinning) {
-         // This check is tricky because ora() creates a new instance. 
-         // We'll just log the error.
+        // This check is tricky because ora() creates a new instance.
+        // We'll just log the error.
       }
       console.error(chalk.red('\nExtraction failed:'));
       console.error((error as Error).message);
@@ -95,7 +99,7 @@ program
   });
 
 program
-   .command('mcp')
+  .command('mcp')
   .description('Start MCP server')
   .action(async () => {
     const { startMCPServer } = await import('./mcp/server.js');

packages/cli/src/mcp/server.ts

@@ -1,22 +1,22 @@
+import type { Config } from '@doc-agent/core';
+import { extractDocument } from '@doc-agent/extract';
 import { Server } from '@modelcontextprotocol/sdk/server';
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
 import {
+  type CallToolRequest,
   CallToolRequestSchema,
   ListToolsRequestSchema,
-  CallToolRequest
 } from '@modelcontextprotocol/sdk/types.js';
-import { extractDocument } from '@doc-agent/extract';
-import type { Config } from '@doc-agent/core';
 
 const server = new Server(
   {
     name: 'doc-agent',
-    version: '0.1.0'
+    version: '0.1.0',
   },
   {
     capabilities: {
-      tools: {}
-    }
+      tools: {},
+    },
   }
 );
 
@@ -32,17 +32,17 @@ server.setRequestHandler(ListToolsRequestSchema, async () => {
           properties: {
             filepath: {
               type: 'string',
-              description: 'Path to the document file'
+              description: 'Path to the document file',
             },
             provider: {
               type: 'string',
               enum: ['gemini', 'openai', 'ollama'],
               description: 'AI provider to use',
-              default: 'gemini'
-            }
+              default: 'gemini',
+            },
           },
-          required: ['filepath']
-        }
+          required: ['filepath'],
+        },
       },
       {
         name: 'search_documents',
@@ -52,18 +52,18 @@ server.setRequestHandler(ListToolsRequestSchema, async () => {
           properties: {
             query: {
               type: 'string',
-              description: 'Search query in natural language'
+              description: 'Search query in natural language',
             },
             limit: {
               type: 'number',
               description: 'Maximum number of results',
-              default: 10
-            }
+              default: 10,
+            },
           },
-          required: ['query']
-        }
-      }
-    ]
+          required: ['query'],
+        },
+      },
+    ],
   };
 });
 
@@ -74,48 +74,48 @@ server.setRequestHandler(CallToolRequestSchema, async (request: CallToolRequest)
       filepath: string;
       provider?: string;
     };
-    
+
     const config: Config = {
       aiProvider: provider as 'gemini' | 'openai' | 'ollama',
       geminiApiKey: process.env.GEMINI_API_KEY,
-      openaiApiKey: process.env.OPENAI_API_KEY
+      openaiApiKey: process.env.OPENAI_API_KEY,
     };
-    
+
     try {
       const result = await extractDocument(filepath, config);
-      
+
       return {
         content: [
           {
             type: 'text',
-            text: JSON.stringify(result, null, 2)
-          }
-        ]
+            text: JSON.stringify(result, null, 2),
+          },
+        ],
       };
     } catch (error) {
       return {
         content: [
           {
             type: 'text',
-            text: `Error: ${(error as Error).message}`
-          }
+            text: `Error: ${(error as Error).message}`,
+          },
         ],
-        isError: true
+        isError: true,
       };
     }
   }
-  
+
   if (request.params.name === 'search_documents') {
     return {
       content: [
         {
           type: 'text',
-          text: 'Search functionality not yet implemented'
-        }
-      ]
+          text: 'Search functionality not yet implemented',
+        },
+      ],
     };
   }
-  
+
   throw new Error(`Unknown tool: ${request.params.name}`);
 });
 

packages/cli/tsconfig.json

@@ -6,9 +6,5 @@
   },
   "include": ["src/**/*"],
   "exclude": ["node_modules", "dist"],
-  "references": [
-    { "path": "../core" },
-    { "path": "../extract" },
-    { "path": "../vector-store" }
-  ]
+  "references": [{ "path": "../core" }, { "path": "../extract" }, { "path": "../vector-store" }]
 }

packages/core/package.json

@@ -26,4 +26,4 @@
   "devDependencies": {
     "typescript": "^5.9.3"
   }
-}
+}