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

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 */ }