fix: Use bare codegraph everywhere, add preuninstall cleanup

- Revert configs (MCP, hooks) to use bare `codegraph` command
- Remove all npx references from configs and messaging
- Add preuninstall script that runs on `npm uninstall -g` to clean up
  MCP server, permissions, hooks, and CLAUDE.md section
- Show uninstall instructions in post-install next steps

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@colbymchenry/codegraph",
-  "version": "0.5.5",
+  "version": "0.6.0",
   "description": "Supercharge Claude Code with semantic code intelligence. 30% fewer tokens, 25% fewer tool calls, 100% local.",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -15,6 +15,7 @@
   "scripts": {
     "build": "tsc && npm run copy-assets",
     "postinstall": "node scripts/postinstall.js",
+    "preuninstall": "node dist/bin/uninstall.js",
     "copy-assets": "node -e \"const fs=require('fs');fs.mkdirSync('dist/db',{recursive:true});fs.copyFileSync('src/db/schema.sql','dist/db/schema.sql');fs.mkdirSync('dist/extraction/wasm',{recursive:true});fs.readdirSync('src/extraction/wasm').filter(f=>f.endsWith('.wasm')).forEach(f=>fs.copyFileSync('src/extraction/wasm/'+f,'dist/extraction/wasm/'+f))\"",
     "dev": "tsc --watch",
     "cli": "npm run build && node dist/bin/codegraph.js",

src/bin/uninstall.ts

@@ -0,0 +1,151 @@
+#!/usr/bin/env node
+/**
+ * CodeGraph preuninstall cleanup script
+ *
+ * Runs automatically when `npm uninstall -g @colbymchenry/codegraph` is called.
+ * Removes all CodeGraph configuration from Claude Code:
+ *   - MCP server entry from ~/.claude.json
+ *   - Permissions from ~/.claude/settings.json
+ *   - Hooks from ~/.claude/settings.json
+ *   - CodeGraph section from ~/.claude/CLAUDE.md
+ *
+ * This script must never throw — a failed cleanup must not block uninstall.
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+
+const CODEGRAPH_SECTION_START = '<!-- CODEGRAPH_START -->';
+const CODEGRAPH_SECTION_END = '<!-- CODEGRAPH_END -->';
+
+function readJson(filePath: string): Record<string, any> | null {
+  try {
+    if (!fs.existsSync(filePath)) return null;
+    return JSON.parse(fs.readFileSync(filePath, 'utf-8'));
+  } catch {
+    return null;
+  }
+}
+
+function writeJson(filePath: string, data: Record<string, any>): void {
+  fs.writeFileSync(filePath, JSON.stringify(data, null, 2) + '\n');
+}
+
+/**
+ * Remove CodeGraph MCP server from ~/.claude.json
+ */
+function removeMcpConfig(): void {
+  const filePath = path.join(os.homedir(), '.claude.json');
+  const config = readJson(filePath);
+  if (!config?.mcpServers?.codegraph) return;
+
+  delete config.mcpServers.codegraph;
+
+  // Clean up empty mcpServers object
+  if (Object.keys(config.mcpServers).length === 0) {
+    delete config.mcpServers;
+  }
+
+  writeJson(filePath, config);
+}
+
+/**
+ * Remove CodeGraph permissions and hooks from ~/.claude/settings.json
+ */
+function removeSettings(): void {
+  const filePath = path.join(os.homedir(), '.claude', 'settings.json');
+  const settings = readJson(filePath);
+  if (!settings) return;
+
+  let changed = false;
+
+  // Remove codegraph permissions
+  if (Array.isArray(settings.permissions?.allow)) {
+    const before = settings.permissions.allow.length;
+    settings.permissions.allow = settings.permissions.allow.filter(
+      (p: string) => !p.startsWith('mcp__codegraph__')
+    );
+    if (settings.permissions.allow.length !== before) changed = true;
+
+    // Clean up empty allow array
+    if (settings.permissions.allow.length === 0) {
+      delete settings.permissions.allow;
+    }
+    // Clean up empty permissions object
+    if (Object.keys(settings.permissions).length === 0) {
+      delete settings.permissions;
+    }
+  }
+
+  // Remove codegraph hooks
+  if (settings.hooks) {
+    for (const event of Object.keys(settings.hooks)) {
+      if (!Array.isArray(settings.hooks[event])) continue;
+
+      const before = settings.hooks[event].length;
+      settings.hooks[event] = settings.hooks[event].filter((entry: any) => {
+        const json = JSON.stringify(entry);
+        return !json.includes('codegraph mark-dirty') && !json.includes('codegraph sync-if-dirty');
+      });
+      if (settings.hooks[event].length !== before) changed = true;
+
+      // Clean up empty event arrays
+      if (settings.hooks[event].length === 0) {
+        delete settings.hooks[event];
+      }
+    }
+
+    // Clean up empty hooks object
+    if (Object.keys(settings.hooks).length === 0) {
+      delete settings.hooks;
+    }
+  }
+
+  if (changed) {
+    writeJson(filePath, settings);
+  }
+}
+
+/**
+ * Remove CodeGraph section from ~/.claude/CLAUDE.md
+ */
+function removeClaudeMd(): void {
+  const filePath = path.join(os.homedir(), '.claude', 'CLAUDE.md');
+  try {
+    if (!fs.existsSync(filePath)) return;
+    let content = fs.readFileSync(filePath, 'utf-8');
+
+    // Remove marked section
+    const startIdx = content.indexOf(CODEGRAPH_SECTION_START);
+    const endIdx = content.indexOf(CODEGRAPH_SECTION_END);
+
+    if (startIdx !== -1 && endIdx > startIdx) {
+      const before = content.substring(0, startIdx).trimEnd();
+      const after = content.substring(endIdx + CODEGRAPH_SECTION_END.length).trimStart();
+      content = before + (before && after ? '\n\n' : '') + after;
+
+      if (content.trim() === '') {
+        // File is empty after removing section — delete it
+        fs.unlinkSync(filePath);
+      } else {
+        fs.writeFileSync(filePath, content.trim() + '\n');
+      }
+    }
+  } catch {
+    // Never fail
+  }
+}
+
+// Run cleanup — never throw
+try {
+  removeMcpConfig();
+} catch { /* ignore */ }
+
+try {
+  removeSettings();
+} catch { /* ignore */ }
+
+try {
+  removeClaudeMd();
+} catch { /* ignore */ }

src/installer/banner.ts

@@ -113,21 +113,18 @@ export function warn(message: string): void {
 /**
  * Show the "next steps" section after installation
  */
-export function showNextSteps(location: 'global' | 'local', codegraphAvailable?: boolean): void {
+export function showNextSteps(location: 'global' | 'local'): void {
   console.log();
   console.log(chalk.bold('  Done!') + ' Restart Claude Code to use CodeGraph.');
   console.log();
 
   if (location === 'global') {
-    const cmd = codegraphAvailable ? 'codegraph' : 'npx @colbymchenry/codegraph';
     console.log(chalk.dim('  Quick start:'));
     console.log(chalk.dim('    cd your-project'));
-    console.log(chalk.cyan(`    ${cmd} init -i`));
+    console.log(chalk.cyan('    codegraph init -i'));
-    if (!codegraphAvailable) {
     console.log();
-      console.log(chalk.dim('  Tip: For a shorter command, install globally:'));
+    console.log(chalk.dim('  To uninstall:'));
-      console.log(chalk.dim('    npm install -g @colbymchenry/codegraph'));
+    console.log(chalk.dim('    npm uninstall -g @colbymchenry/codegraph'));
-    }
   } else {
     console.log(chalk.dim('  CodeGraph is ready to use in this project!'));
   }

src/installer/config-writer.ts

@@ -98,13 +98,13 @@ function writeJsonFile(filePath: string, data: Record<string, any>): void {
 }
 
 /**
- * Get the MCP server configuration — always uses npx for reliability
+ * Get the MCP server configuration
  */
 function getMcpServerConfig(): Record<string, any> {
   return {
     type: 'stdio',
-    command: 'npx',
+    command: 'codegraph',
-    args: ['@colbymchenry/codegraph', 'serve', '--mcp'],
+    args: ['serve', '--mcp'],
   };
 }
 
@@ -203,7 +203,7 @@ export function hasPermissions(location: InstallLocation): boolean {
  * Stop → sync-if-dirty (sync, ensures fresh index before next user turn)
  */
 function getHooksConfig(): Record<string, any> {
-  const command = 'npx @colbymchenry/codegraph';
+  const command = 'codegraph';
 
   return {
     PostToolUse: [

src/installer/index.ts

@@ -25,13 +25,10 @@ export async function runInstaller(): Promise<void> {
   showBanner();
 
   try {
-    // Step 1: Try global install for bare `codegraph` command convenience.
+    // Step 1: Ensure codegraph is installed globally
-    // This is best-effort — configs always use npx regardless.
-    let codegraphAvailable = false;
     try {
       const checkCmd = process.platform === 'win32' ? 'where codegraph' : 'command -v codegraph';
       execSync(checkCmd, { stdio: 'pipe' });
-      codegraphAvailable = true;
     } catch {
       // Not installed globally yet — try to install
       console.log(chalk.dim('  Installing codegraph globally...'));
@@ -40,18 +37,16 @@ export async function runInstaller(): Promise<void> {
         // Verify it actually worked (PATH may not include npm global bin)
         try {
           execSync(process.platform === 'win32' ? 'where codegraph' : 'command -v codegraph', { stdio: 'pipe' });
-          codegraphAvailable = true;
           success('Installed codegraph command globally');
         } catch {
           // Install "succeeded" but command not in PATH — common with nvm/fnm
           info('Global install succeeded but codegraph is not in your PATH');
-          info('You may need to add npm\'s global bin to your PATH, or use:');
+          info('You may need to add npm\'s global bin directory to your PATH');
-          info('  npx @colbymchenry/codegraph <command>');
+          info('Then restart your terminal and run: codegraph init -i');
         }
       } catch {
         info('Could not install globally (permission denied)');
-        info('You can install manually with: sudo npm install -g @colbymchenry/codegraph');
+        info('Try: sudo npm install -g @colbymchenry/codegraph');
-        info('Or use: npx @colbymchenry/codegraph <command>');
       }
       console.log();
     }
@@ -113,7 +108,7 @@ export async function runInstaller(): Promise<void> {
     }
 
     // Show next steps
-    showNextSteps(location, codegraphAvailable);
+    showNextSteps(location);
   } catch (err) {
     console.log();
     if (err instanceof Error && err.message.includes('readline was closed')) {
@@ -139,7 +134,7 @@ async function initializeLocalProject(): Promise<void> {
   } catch (err) {
     const msg = err instanceof Error ? err.message : String(err);
     error(`Could not load native modules: ${msg}`);
-    info('Skipping project initialization. You can run "npx @colbymchenry/codegraph init -i" later.');
+    info('Skipping project initialization. You can run "codegraph init -i" later.');
     info('If this persists, try a Node.js LTS version (20 or 22).');
     return;
   }