refactor(mcp): migrate adapters to service layer with dependency injection

.gitignore

@@ -70,3 +70,4 @@ packages/benchmark/
 
 # Benchmark studies and session logs
 studies/
+.test-vectors/

AGENTS.md

@@ -167,7 +167,7 @@ Command-line interface for repository indexing and MCP setup.
 - `dev mcp install [--cursor]` - Install MCP integration
 - `dev mcp uninstall [--cursor]` - Remove MCP integration
 - `dev mcp list [--cursor]` - List MCP servers
-- `dev gh index` - Index GitHub issues/PRs
+- `dev github index` - Index GitHub issues/PRs
 
 ### @lytics/dev-agent-subagents
 
@@ -391,7 +391,7 @@ pnpm dev                                  # Watch mode
 pnpm lint && pnpm typecheck              # Quality checks
 dev index .                              # Index repository
 dev mcp install --cursor                 # Install for Cursor
-dev gh index                             # Index GitHub
+dev github index                             # Index GitHub
 
 # Debugging
 dev mcp start --verbose                  # Verbose MCP server

CHANGELOG.md

@@ -50,7 +50,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 - Memory leaks from unbounded array growth
 - Zombie MCP server processes when Cursor closes
-- GitHub index not reloading after `dev gh index`
+- GitHub index not reloading after `dev github index`
 - STDIO transport not handling stdin closure properly
 
 ### Security
@@ -104,7 +104,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
    ```bash
    cd /path/to/repo
    dev index .
-   dev gh index  # If using GitHub integration
+   dev github index  # If using GitHub integration
    ```
 
 3. Reinstall MCP integration:

README.md

@@ -244,8 +244,8 @@ dev git search "authentication fix"   # Semantic search over commits
 dev git stats                         # Show indexed commit count
 
 # GitHub integration
-dev gh index                          # Index issues and PRs (also done by dev index)
-dev gh search "authentication bug"    # Semantic search
+dev github index                          # Index issues and PRs (also done by dev index)
+dev github search "authentication bug"    # Semantic search
 
 # View statistics
 dev stats

TROUBLESHOOTING.md

@@ -350,7 +350,7 @@ dev index .
 
 ## GitHub Integration
 
-### `dev gh index` fails
+### `dev github index` fails
 
 **Common causes:**
 
@@ -386,7 +386,7 @@ Failed to fetch issues: spawnSync /bin/sh ENOBUFS
    dev index --gh-limit 100
 
    # For dedicated GitHub indexing
-   dev gh index --limit 100
+   dev github index --limit 100
    ```
 
 2. **Adjust limit based on repository size:**
@@ -397,10 +397,10 @@ Failed to fetch issues: spawnSync /bin/sh ENOBUFS
 3. **Index in batches:**
    ```bash
    # Index open items only (usually smaller)
-   dev gh index --state open --limit 500
+   dev github index --state open --limit 500
 
    # Then index closed items with lower limit
-   dev gh index --state closed --limit 100
+   dev github index --state closed --limit 100
    ```
 
 **Technical details:**
@@ -424,10 +424,10 @@ Failed to fetch issues: spawnSync /bin/sh ENOBUFS
 
 3. **Re-index:**
    ```bash
-   dev gh index
+   dev github index
    ```
 
-**Note:** The `dev_gh` tool automatically reloads when you run `dev gh index` - no restart needed!
+**Note:** The `dev_gh` tool automatically reloads when you run `dev github index` - no restart needed!
 
 ### GitHub index is stale
 
@@ -438,13 +438,13 @@ Use dev_health tool - warns if GitHub index >24h old
 
 **Solution:**
 ```bash
-dev gh index
+dev github index
 ```
 
 **Automation (optional):**
 ```bash
 # Add to crontab for daily updates
-0 9 * * * cd /path/to/repo && dev gh index
+0 9 * * * cd /path/to/repo && dev github index
 ```
 
 ---
@@ -534,7 +534,7 @@ Use dev_health tool to check component status
 ```bash
 # Re-index everything
 dev index .
-dev gh index
+dev github index
 
 # Restart MCP server
 ```
@@ -689,7 +689,7 @@ rm -rf ~/.dev-agent/indexes/*
 # Re-index your repositories
 cd /path/to/your/repo
 dev index .
-dev gh index
+dev github index
 
 # Reinstall MCP
 dev mcp install --cursor  # or without --cursor for Claude Code
@@ -755,7 +755,7 @@ npm update -g dev-agent
 # Re-index repositories (recommended)
 cd /path/to/your/repo
 dev index .
-dev gh index
+dev github index
 
 # Restart AI tool
 ```
@@ -944,7 +944,7 @@ dev index .
 
 **GitHub Index Stale:**
 ```bash
-dev gh index
+dev github index
 ```
 
 **Repository Not Accessible:**

WORKFLOW.md

@@ -20,7 +20,7 @@ git checkout main
 git pull origin main
 
 # Use GitHub Context to find what to work on next
-dev gh search "state:open label:\"Epic: MCP Integration\"" --type issue
+dev github search "state:open label:\"Epic: MCP Integration\"" --type issue
 
 # Or use gh CLI directly
 gh issue list --milestone "Epic #3: MCP Integration" --state open

examples/README.md

@@ -195,7 +195,7 @@ dev_gh:
 
 **First, index GitHub:**
 ```bash
-dev gh index
+dev github index
 ```
 
 ---
@@ -339,7 +339,7 @@ dev_health:
 dev index .
 
 # After new issues/PRs
-dev gh index
+dev github index
 
 # Check health
 dev_health

packages/cli/CHANGELOG.md

@@ -98,7 +98,7 @@
 
   **Indexer Logging**
 
-  - Add `--verbose` flag to `dev index`, `dev git index`, `dev gh index`
+  - Add `--verbose` flag to `dev index`, `dev git index`, `dev github index`
   - Progress spinner shows actual counts: `Embedding 4480/49151 documents (9%)`
   - Structured logging with kero logger
 

packages/cli/src/cli.test.ts

@@ -58,16 +58,9 @@ describe('CLI Structure', () => {
       expect(jsonOption).toBeDefined();
     });
 
-    it('stats command should have show subcommand with json option', () => {
-      const subcommands = statsCommand.commands;
-      const showCommand = subcommands.find((cmd) => cmd.name() === 'show');
-
-      expect(showCommand).toBeDefined();
-
-      if (showCommand) {
-        const jsonOption = showCommand.options.find((opt) => opt.long === '--json');
-        expect(jsonOption).toBeDefined();
-      }
+    it('stats command should have json option', () => {
+      const jsonOption = statsCommand.options.find((opt) => opt.long === '--json');
+      expect(jsonOption).toBeDefined();
     });
 
     it('clean command should have force option', () => {

packages/cli/src/cli.ts

@@ -6,8 +6,8 @@ import { cleanCommand } from './commands/clean.js';
 import { compactCommand } from './commands/compact.js';
 import { dashboardCommand } from './commands/dashboard.js';
 import { exploreCommand } from './commands/explore.js';
-import { ghCommand } from './commands/gh.js';
 import { gitCommand } from './commands/git.js';
+import { githubCommand } from './commands/github.js';
 import { indexCommand } from './commands/index.js';
 import { initCommand } from './commands/init.js';
 import { mcpCommand } from './commands/mcp.js';
@@ -35,7 +35,7 @@ program.addCommand(indexCommand);
 program.addCommand(searchCommand);
 program.addCommand(exploreCommand);
 program.addCommand(planCommand);
-program.addCommand(ghCommand);
+program.addCommand(githubCommand);
 program.addCommand(gitCommand);
 program.addCommand(updateCommand);
 program.addCommand(statsCommand);

packages/cli/src/commands/clean.ts

@@ -5,11 +5,12 @@ import {
   getStorageFilePaths,
   getStoragePath,
 } from '@lytics/dev-agent-core';
-import chalk from 'chalk';
 import { Command } from 'commander';
 import ora from 'ora';
 import { loadConfig } from '../utils/config.js';
+import { getDirectorySize } from '../utils/file.js';
 import { logger } from '../utils/logger.js';
+import { output, printCleanSuccess, printCleanSummary } from '../utils/output.js';
 
 export const cleanCommand = new Command('clean')
   .description('Clean indexed data and cache')
@@ -33,21 +34,35 @@ export const cleanCommand = new Command('clean')
       await ensureStorageDirectory(storagePath);
       const filePaths = getStorageFilePaths(storagePath);
 
+      // Calculate sizes of files to be deleted
+      const files = await Promise.all(
+        [
+          { name: 'Vector store', path: filePaths.vectors },
+          { name: 'Indexer state', path: filePaths.indexerState },
+          { name: 'GitHub state', path: filePaths.githubState },
+          { name: 'Metadata', path: filePaths.metadata },
+        ].map(async (file) => {
+          try {
+            const stat = await fs.stat(file.path);
+            const size = stat.isDirectory() ? await getDirectorySize(file.path) : stat.size;
+            return { ...file, size };
+          } catch {
+            return { ...file, size: null };
+          }
+        })
+      );
+
+      const totalSize = files.reduce((sum, file) => sum + (file.size || 0), 0);
+
       // Show what will be deleted
-      logger.log('');
-      logger.log(chalk.bold('The following will be deleted:'));
-      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('');
+      printCleanSummary({
+        files,
+        totalSize,
+        force: options.force,
+      });
 
       // Confirm unless --force
       if (!options.force) {
-        logger.warn('This action cannot be undone!');
-        logger.log(`Run with ${chalk.yellow('--force')} to skip this prompt.`);
-        logger.log('');
         process.exit(0);
       }
 
@@ -56,17 +71,14 @@ export const cleanCommand = new Command('clean')
       // Delete storage directory (contains all index files)
       try {
         await fs.rm(storagePath, { recursive: true, force: true });
-        spinner.succeed(chalk.green('Cleaned successfully!'));
+        spinner.succeed('Cleaned successfully');
+
+        printCleanSuccess({ totalSize });
       } catch (error) {
         spinner.fail('Failed to clean');
-        logger.error(`Error: ${error instanceof Error ? error.message : String(error)}`);
+        output.error(`Error: ${error instanceof Error ? error.message : String(error)}`);
         process.exit(1);
       }
-
-      logger.log('');
-      logger.log('All indexed data has been removed.');
-      logger.log(`Run ${chalk.yellow('dev index')} to re-index your repository.`);
-      logger.log('');
     } catch (error) {
       logger.error(`Failed to clean: ${error instanceof Error ? error.message : String(error)}`);
       process.exit(1);

packages/cli/src/commands/compact.ts

@@ -5,11 +5,11 @@ import {
   getStoragePath,
   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';
+import { printCompactResults } from '../utils/output.js';
 
 export const compactCommand = new Command('compact')
   .description('🗜️  Optimize and compact the vector store')
@@ -65,36 +65,25 @@ export const compactCommand = new Command('compact')
       // @ts-expect-error - accessing private property for optimization
       await indexer.vectorStorage.optimize();
 
-      const duration = ((Date.now() - startTime) / 1000).toFixed(2);
+      const duration = (Date.now() - startTime) / 1000;
 
       // Get stats after optimization
       const statsAfter = await indexer.getStats();
 
       await indexer.close();
 
-      spinner.succeed(chalk.green('Vector store optimized successfully!'));
-
-      // Show results
-      logger.log('');
-      logger.log(chalk.bold('Optimization Results:'));
-      logger.log(`  ${chalk.cyan('Duration:')}        ${duration}s`);
-      logger.log(`  ${chalk.cyan('Total documents:')} ${statsAfter?.vectorsStored || 0}`);
-
-      if (options.verbose) {
-        logger.log('');
-        logger.log(chalk.bold('Before Optimization:'));
-        logger.log(`  ${chalk.cyan('Storage size:')} ${statsBefore.vectorsStored} vectors`);
-        logger.log('');
-        logger.log(chalk.bold('After Optimization:'));
-        logger.log(`  ${chalk.cyan('Storage size:')} ${statsAfter?.vectorsStored || 0} vectors`);
-      }
-
-      logger.log('');
-      logger.log(
-        chalk.gray(
-          'Optimization merges small data fragments, updates indices, and improves query performance.'
-        )
-      );
+      spinner.succeed('Vector store optimized');
+
+      // Show results using new formatter
+      printCompactResults({
+        duration,
+        before: {
+          vectors: statsBefore.vectorsStored,
+        },
+        after: {
+          vectors: statsAfter?.vectorsStored || 0,
+        },
+      });
     } catch (error) {
       spinner.fail('Failed to optimize vector store');
       logger.error(error instanceof Error ? error.message : String(error));