feat: Foundation - Storage + Config System (Issue #52)

packages/cli/src/cli.ts

@@ -11,6 +11,7 @@ import { initCommand } from './commands/init.js';
 import { planCommand } from './commands/plan.js';
 import { searchCommand } from './commands/search.js';
 import { statsCommand } from './commands/stats.js';
+import { storageCommand } from './commands/storage.js';
 import { updateCommand } from './commands/update.js';
 
 const program = new Command();
@@ -31,6 +32,7 @@ program.addCommand(updateCommand);
 program.addCommand(statsCommand);
 program.addCommand(compactCommand);
 program.addCommand(cleanCommand);
+program.addCommand(storageCommand);
 
 // Show help if no command provided
 if (process.argv.length === 2) {

packages/cli/src/commands/clean.ts

@@ -1,5 +1,10 @@
 import * as fs from 'node:fs/promises';
 import * as path from 'node:path';
+import {
+  ensureStorageDirectory,
+  getStorageFilePaths,
+  getStoragePath,
+} from '@lytics/dev-agent-core';
 import chalk from 'chalk';
 import { Command } from 'commander';
 import ora from 'ora';
@@ -19,15 +24,23 @@ export const cleanCommand = new Command('clean')
         return;
       }
 
-      const dataDir = path.dirname(config.vectorStorePath);
-      const stateFile = path.join(config.repositoryPath, '.dev-agent', 'indexer-state.json');
+      // Resolve repository path
+      const repositoryPath = config.repository?.path || config.repositoryPath || process.cwd();
+      const resolvedRepoPath = path.resolve(repositoryPath);
+
+      // Get centralized storage paths
+      const storagePath = await getStoragePath(resolvedRepoPath);
+      await ensureStorageDirectory(storagePath);
+      const filePaths = getStorageFilePaths(storagePath);
 
       // Show what will be deleted
       logger.log('');
       logger.log(chalk.bold('The following will be deleted:'));
-      logger.log(`  ${chalk.cyan('Vector store:')} ${config.vectorStorePath}`);
-      logger.log(`  ${chalk.cyan('State file:')}   ${stateFile}`);
-      logger.log(`  ${chalk.cyan('Data directory:')} ${dataDir}`);
+      logger.log(`  ${chalk.cyan('Storage directory:')} ${storagePath}`);
+      logger.log(`  ${chalk.cyan('Vector store:')}     ${filePaths.vectors}`);
+      logger.log(`  ${chalk.cyan('State file:')}       ${filePaths.indexerState}`);
+      logger.log(`  ${chalk.cyan('GitHub state:')}      ${filePaths.githubState}`);
+      logger.log(`  ${chalk.cyan('Metadata:')}         ${filePaths.metadata}`);
       logger.log('');
 
       // Confirm unless --force
@@ -40,35 +53,16 @@ export const cleanCommand = new Command('clean')
 
       const spinner = ora('Cleaning indexed data...').start();
 
-      // Delete vector store
-      try {
-        await fs.rm(config.vectorStorePath, { recursive: true, force: true });
-        spinner.text = 'Deleted vector store';
-      } catch (error) {
-        logger.debug(`Vector store not found or already deleted: ${error}`);
-      }
-
-      // Delete state file
+      // Delete storage directory (contains all index files)
       try {
-        await fs.rm(stateFile, { force: true });
-        spinner.text = 'Deleted state file';
+        await fs.rm(storagePath, { recursive: true, force: true });
+        spinner.succeed(chalk.green('Cleaned successfully!'));
       } catch (error) {
-        logger.debug(`State file not found or already deleted: ${error}`);
+        spinner.fail('Failed to clean');
+        logger.error(`Error: ${error instanceof Error ? error.message : String(error)}`);
+        process.exit(1);
       }
 
-      // Delete data directory if empty
-      try {
-        const files = await fs.readdir(dataDir);
-        if (files.length === 0) {
-          await fs.rmdir(dataDir);
-          spinner.text = 'Deleted data directory';
-        }
-      } catch (error) {
-        logger.debug(`Data directory not found or not empty: ${error}`);
-      }
-
-      spinner.succeed(chalk.green('Cleaned successfully!'));
-
       logger.log('');
       logger.log('All indexed data has been removed.');
       logger.log(`Run ${chalk.yellow('dev index')} to re-index your repository.`);

packages/cli/src/commands/commands.test.ts

@@ -36,7 +36,7 @@ describe('CLI Commands', () => {
       exitSpy.mockRestore();
 
       // Check config file was created
-      const configPath = path.join(initDir, '.dev-agent.json');
+      const configPath = path.join(initDir, '.dev-agent', 'config.json');
       const exists = await fs
         .access(configPath)
         .then(() => true)
@@ -46,6 +46,9 @@ describe('CLI Commands', () => {
       // Verify config content
       const content = await fs.readFile(configPath, 'utf-8');
       const config = JSON.parse(content);
+      expect(config.version).toBe('1.0');
+      expect(config.repository).toBeDefined();
+      // Legacy fields for backward compatibility
       expect(config.repositoryPath).toBe(path.resolve(initDir));
       expect(config.embeddingModel).toBe('Xenova/all-MiniLM-L6-v2');
     });

packages/cli/src/commands/compact.ts

@@ -1,4 +1,10 @@
-import { RepositoryIndexer } from '@lytics/dev-agent-core';
+import * as path from 'node:path';
+import {
+  ensureStorageDirectory,
+  getStorageFilePaths,
+  getStoragePath,
+  RepositoryIndexer,
+} from '@lytics/dev-agent-core';
 import chalk from 'chalk';
 import { Command } from 'commander';
 import ora from 'ora';
@@ -21,8 +27,24 @@ export const compactCommand = new Command('compact')
         return;
       }
 
+      // Resolve repository path
+      const repositoryPath = config.repository?.path || config.repositoryPath || process.cwd();
+      const resolvedRepoPath = path.resolve(repositoryPath);
+
+      // Get centralized storage paths
+      const storagePath = await getStoragePath(resolvedRepoPath);
+      await ensureStorageDirectory(storagePath);
+      const filePaths = getStorageFilePaths(storagePath);
+
       spinner.text = 'Initializing indexer...';
-      const indexer = new RepositoryIndexer(config);
+      const indexer = new RepositoryIndexer({
+        repositoryPath: resolvedRepoPath,
+        vectorStorePath: filePaths.vectors,
+        statePath: filePaths.indexerState,
+        excludePatterns: config.repository?.excludePatterns || config.excludePatterns,
+        languages: config.repository?.languages || config.languages,
+      });
+
       await indexer.initialize();
 
       // Get stats before optimization

packages/cli/src/commands/explore.ts

@@ -1,4 +1,10 @@
-import { RepositoryIndexer } from '@lytics/dev-agent-core';
+import * as path from 'node:path';
+import {
+  ensureStorageDirectory,
+  getStorageFilePaths,
+  getStoragePath,
+  RepositoryIndexer,
+} from '@lytics/dev-agent-core';
 import chalk from 'chalk';
 import { Command } from 'commander';
 import ora from 'ora';
@@ -26,7 +32,23 @@ explore
         return;
       }
 
-      const indexer = new RepositoryIndexer(config);
+      // Resolve repository path
+      const repositoryPath = config.repository?.path || config.repositoryPath || process.cwd();
+      const resolvedRepoPath = path.resolve(repositoryPath);
+
+      // Get centralized storage paths
+      const storagePath = await getStoragePath(resolvedRepoPath);
+      await ensureStorageDirectory(storagePath);
+      const filePaths = getStorageFilePaths(storagePath);
+
+      const indexer = new RepositoryIndexer({
+        repositoryPath: resolvedRepoPath,
+        vectorStorePath: filePaths.vectors,
+        statePath: filePaths.indexerState,
+        excludePatterns: config.repository?.excludePatterns || config.excludePatterns,
+        languages: config.repository?.languages || config.languages,
+      });
+
       await indexer.initialize();
 
       spinner.text = `Searching: "${query}"`;
@@ -85,20 +107,36 @@ explore
         return;
       }
 
+      // Resolve repository path
+      const repositoryPath = config.repository?.path || config.repositoryPath || process.cwd();
+      const resolvedRepoPath = path.resolve(repositoryPath);
+
+      // Get centralized storage paths
+      const storagePath = await getStoragePath(resolvedRepoPath);
+      await ensureStorageDirectory(storagePath);
+      const filePaths = getStorageFilePaths(storagePath);
+
       // Prepare file for search (read content, resolve paths)
       spinner.text = 'Reading file content...';
       const { prepareFileForSearch } = await import('../utils/file.js');
 
       let fileInfo: Awaited<ReturnType<typeof prepareFileForSearch>>;
       try {
-        fileInfo = await prepareFileForSearch(config.repositoryPath, file);
+        fileInfo = await prepareFileForSearch(resolvedRepoPath, file);
       } catch (error) {
         spinner.fail((error as Error).message);
         process.exit(1);
         return;
       }
 
-      const indexer = new RepositoryIndexer(config);
+      const indexer = new RepositoryIndexer({
+        repositoryPath: resolvedRepoPath,
+        vectorStorePath: filePaths.vectors,
+        statePath: filePaths.indexerState,
+        excludePatterns: config.repository?.excludePatterns || config.excludePatterns,
+        languages: config.repository?.languages || config.languages,
+      });
+
       await indexer.initialize();
 
       // Search using file content, not filename
@@ -124,15 +162,18 @@ explore
         return;
       }
 
-      console.log(chalk.cyan(`\n🔗 Similar to: ${file}\n`));
+      console.log(chalk.cyan(`\n🔍 Similar Code to: ${file}\n`));
 
       for (const [i, result] of similar.entries()) {
         const meta = result.metadata as {
           path: string;
+          name?: string;
           type: string;
+          startLine?: number;
         };
 
-        console.log(chalk.white(`${i + 1}. ${meta.path}`));
+        console.log(chalk.white(`${i + 1}. ${meta.name || meta.type}`));
+        console.log(chalk.gray(`   ${meta.path}${meta.startLine ? `:${meta.startLine}` : ''}`));
         console.log(chalk.green(`   ${(result.score * 100).toFixed(1)}% similar\n`));
       }
 

packages/cli/src/commands/index.ts

@@ -1,4 +1,10 @@
-import { RepositoryIndexer } from '@lytics/dev-agent-core';
+import {
+  ensureStorageDirectory,
+  getStorageFilePaths,
+  getStoragePath,
+  RepositoryIndexer,
+  updateIndexedStats,
+} from '@lytics/dev-agent-core';
 import chalk from 'chalk';
 import { Command } from 'commander';
 import ora from 'ora';
@@ -21,11 +27,26 @@ export const indexCommand = new Command('index')
         config = getDefaultConfig(repositoryPath);
       }
 
-      // Override with command line args
-      config.repositoryPath = repositoryPath;
+      // Override repository path with command line arg
+      const resolvedRepoPath = repositoryPath;
+
+      // Get centralized storage path
+      spinner.text = 'Resolving storage path...';
+      const storagePath = await getStoragePath(resolvedRepoPath);
+      await ensureStorageDirectory(storagePath);
+      const filePaths = getStorageFilePaths(storagePath);
 
       spinner.text = 'Initializing indexer...';
-      const indexer = new RepositoryIndexer(config);
+      const indexer = new RepositoryIndexer({
+        repositoryPath: resolvedRepoPath,
+        vectorStorePath: filePaths.vectors,
+        statePath: filePaths.indexerState,
+        excludePatterns: config.repository?.excludePatterns || config.excludePatterns,
+        languages: config.repository?.languages || config.languages,
+        embeddingModel: config.embeddingModel,
+        embeddingDimension: config.dimension,
+      });
+
       await indexer.initialize();
 
       spinner.text = 'Scanning repository...';
@@ -47,6 +68,13 @@ export const indexCommand = new Command('index')
         },
       });
 
+      // Update metadata with indexing stats
+      await updateIndexedStats(storagePath, {
+        files: stats.filesScanned,
+        components: stats.documentsIndexed,
+        size: 0, // TODO: Calculate actual size
+      });
+
       await indexer.close();
 
       const duration = ((Date.now() - startTime) / 1000).toFixed(2);
@@ -61,6 +89,7 @@ export const indexCommand = new Command('index')
       logger.log(`  ${chalk.cyan('Documents indexed:')}   ${stats.documentsIndexed}`);
       logger.log(`  ${chalk.cyan('Vectors stored:')}      ${stats.vectorsStored}`);
       logger.log(`  ${chalk.cyan('Duration:')}            ${duration}s`);
+      logger.log(`  ${chalk.cyan('Storage:')}             ${storagePath}`);
 
       if (stats.errors.length > 0) {
         logger.log('');

packages/cli/src/commands/plan.ts

@@ -3,7 +3,13 @@
  * Generate development plan from GitHub issue
  */
 
-import { RepositoryIndexer } from '@lytics/dev-agent-core';
+import * as path from 'node:path';
+import {
+  ensureStorageDirectory,
+  getStorageFilePaths,
+  getStoragePath,
+  RepositoryIndexer,
+} from '@lytics/dev-agent-core';
 import chalk from 'chalk';
 import { Command } from 'commander';
 import ora from 'ora';
@@ -93,7 +99,23 @@ export const planCommand = new Command('plan')
       if (options.explorer !== false) {
         spinner.text = 'Finding relevant code...';
 
-        const indexer = new RepositoryIndexer(config);
+        // Resolve repository path
+        const repositoryPath = config.repository?.path || config.repositoryPath || process.cwd();
+        const resolvedRepoPath = path.resolve(repositoryPath);
+
+        // Get centralized storage paths
+        const storagePath = await getStoragePath(resolvedRepoPath);
+        await ensureStorageDirectory(storagePath);
+        const filePaths = getStorageFilePaths(storagePath);
+
+        const indexer = new RepositoryIndexer({
+          repositoryPath: resolvedRepoPath,
+          vectorStorePath: filePaths.vectors,
+          statePath: filePaths.indexerState,
+          excludePatterns: config.repository?.excludePatterns || config.excludePatterns,
+          languages: config.repository?.languages || config.languages,
+        });
+
         await indexer.initialize();
 
         for (const task of tasks) {