refactor(explorer): integrate modular utils architecture

Wire up all utility modules with barrel exports and update consumers:

Architecture changes:
- Create utils/index.ts barrel export for clean imports
- Update explorer/index.ts to import from modular utils
- Maintain backward compatibility via re-exports

Integration:
- Add CLI support with 'dev explore' command
- Implement pattern and similar subcommands
- Connect Explorer agent to CLI interface

Documentation:
- Add comprehensive Explorer README with usage examples
- Document all exploration capabilities and CLI usage

Testing:
- Add 33 integration tests for ExplorerAgent
- Total: 99 tests across all utils modules
- 100% coverage on utilities, 85.57% on explorer core

This completes the modular refactoring, providing:
- Clean separation of concerns (metadata → filters/relationships → analysis)
- Tree-shakeable exports for optimal bundling
- Self-contained modules ready for extraction
- Production-ready CLI interface

Closes #11

Author: prosdev

packages/cli/src/cli.ts

@@ -3,6 +3,7 @@
 import chalk from 'chalk';
 import { Command } from 'commander';
 import { cleanCommand } from './commands/clean.js';
+import { exploreCommand } from './commands/explore.js';
 import { indexCommand } from './commands/index.js';
 import { initCommand } from './commands/init.js';
 import { searchCommand } from './commands/search.js';
@@ -20,6 +21,7 @@ program
 program.addCommand(initCommand);
 program.addCommand(indexCommand);
 program.addCommand(searchCommand);
+program.addCommand(exploreCommand);
 program.addCommand(updateCommand);
 program.addCommand(statsCommand);
 program.addCommand(cleanCommand);

packages/cli/src/commands/explore.ts

@@ -0,0 +1,131 @@
+import { RepositoryIndexer } from '@lytics/dev-agent-core';
+import chalk from 'chalk';
+import { Command } from 'commander';
+import ora from 'ora';
+import { loadConfig } from '../utils/config.js';
+import { logger } from '../utils/logger.js';
+
+const explore = new Command('explore').description('🔍 Explore and analyze code patterns');
+
+// Pattern search subcommand
+explore
+  .command('pattern')
+  .description('Search for code patterns using semantic search')
+  .argument('<query>', 'Pattern to search for')
+  .option('-l, --limit <number>', 'Number of results', '10')
+  .option('-t, --threshold <number>', 'Similarity threshold (0-1)', '0.7')
+  .action(async (query: string, options) => {
+    const spinner = ora('Searching for patterns...').start();
+
+    try {
+      const config = await loadConfig();
+      if (!config) {
+        spinner.fail('No config found');
+        logger.error('Run "dev init" first');
+        process.exit(1);
+        return;
+      }
+
+      const indexer = new RepositoryIndexer(config);
+      await indexer.initialize();
+
+      spinner.text = `Searching: "${query}"`;
+      const results = await indexer.search(query, {
+        limit: Number.parseInt(options.limit, 10),
+        scoreThreshold: Number.parseFloat(options.threshold),
+      });
+
+      spinner.succeed(`Found ${results.length} results`);
+
+      if (results.length === 0) {
+        logger.warn('No patterns found');
+        await indexer.close();
+        return;
+      }
+
+      console.log(chalk.cyan(`\n📊 Pattern Results for: "${query}"\n`));
+
+      for (const [i, result] of results.entries()) {
+        const meta = result.metadata as {
+          path: string;
+          name?: string;
+          type: string;
+          startLine?: number;
+        };
+
+        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)}% match\n`));
+      }
+
+      await indexer.close();
+    } catch (error) {
+      spinner.fail('Pattern search failed');
+      logger.error((error as Error).message);
+      process.exit(1);
+    }
+  });
+
+// Similar code subcommand
+explore
+  .command('similar')
+  .description('Find code similar to a file')
+  .argument('<file>', 'File path')
+  .option('-l, --limit <number>', 'Number of results', '5')
+  .action(async (file: string, options) => {
+    const spinner = ora('Finding similar code...').start();
+
+    try {
+      const config = await loadConfig();
+      if (!config) {
+        spinner.fail('No config found');
+        logger.error('Run "dev init" first');
+        process.exit(1);
+        return;
+      }
+
+      const indexer = new RepositoryIndexer(config);
+      await indexer.initialize();
+
+      const results = await indexer.search(file, {
+        limit: Number.parseInt(options.limit, 10) + 1,
+        scoreThreshold: 0.7,
+      });
+
+      // Filter out the file itself
+      const similar = results
+        .filter((r) => {
+          const meta = r.metadata as { path: string };
+          return !meta.path.includes(file);
+        })
+        .slice(0, Number.parseInt(options.limit, 10));
+
+      spinner.succeed(`Found ${similar.length} similar files`);
+
+      if (similar.length === 0) {
+        logger.warn('No similar code found');
+        await indexer.close();
+        return;
+      }
+
+      console.log(chalk.cyan(`\n🔗 Similar to: ${file}\n`));
+
+      for (const [i, result] of similar.entries()) {
+        const meta = result.metadata as {
+          path: string;
+          type: string;
+        };
+
+        console.log(chalk.white(`${i + 1}. ${meta.path}`));
+        console.log(chalk.green(`   ${(result.score * 100).toFixed(1)}% similar\n`));
+      }
+
+      await indexer.close();
+    } catch (error) {
+      spinner.fail('Similar code search failed');
+      logger.error((error as Error).message);
+      process.exit(1);
+    }
+  });
+
+export { explore as exploreCommand };