Installer now creates/updates CLAUDE.md with CodeGraph instructions

- Added claude-md-template.ts with the instructions template
- Installer writes to ~/.claude/CLAUDE.md (global) or ./.claude/CLAUDE.md (local)
- Smart detection: updates existing CodeGraph section or appends if not found
- Uses HTML comment markers for reliable section replacement on upgrades

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

src/installer/config-writer.ts

@@ -1,12 +1,17 @@
 /**
  * Config file writing for the CodeGraph installer
- * Writes to claude.json and settings.json
+ * Writes to claude.json, settings.json, and CLAUDE.md
  */
 
 import * as fs from 'fs';
 import * as path from 'path';
 import * as os from 'os';
 import { InstallLocation } from './prompts';
+import {
+  CLAUDE_MD_TEMPLATE,
+  CODEGRAPH_SECTION_START,
+  CODEGRAPH_SECTION_END,
+} from './claude-md-template';
 
 /**
  * Get the path to the Claude config directory
@@ -169,3 +174,101 @@ export function hasPermissions(location: InstallLocation): boolean {
   // Check if at least one CodeGraph permission exists
   return permissions.some((p: string) => p.startsWith('mcp__codegraph__'));
 }
+
+/**
+ * Get the path to CLAUDE.md
+ * - Global: ~/.claude/CLAUDE.md
+ * - Local: ./.claude/CLAUDE.md
+ */
+function getClaudeMdPath(location: InstallLocation): string {
+  const configDir = getClaudeConfigDir(location);
+  return path.join(configDir, 'CLAUDE.md');
+}
+
+/**
+ * Check if CLAUDE.md has CodeGraph section
+ */
+export function hasClaudeMdSection(location: InstallLocation): boolean {
+  const claudeMdPath = getClaudeMdPath(location);
+  try {
+    if (fs.existsSync(claudeMdPath)) {
+      const content = fs.readFileSync(claudeMdPath, 'utf-8');
+      return content.includes(CODEGRAPH_SECTION_START) || content.includes('## CodeGraph');
+    }
+  } catch {
+    // Ignore errors
+  }
+  return false;
+}
+
+/**
+ * Write or update CLAUDE.md with CodeGraph instructions
+ *
+ * If the file exists and has a CodeGraph section (marked or unmarked),
+ * it will be replaced. Otherwise, the template is appended.
+ */
+export function writeClaudeMd(location: InstallLocation): { created: boolean; updated: boolean } {
+  const claudeMdPath = getClaudeMdPath(location);
+  const configDir = getClaudeConfigDir(location);
+
+  // Ensure directory exists
+  if (!fs.existsSync(configDir)) {
+    fs.mkdirSync(configDir, { recursive: true });
+  }
+
+  // Check if file exists
+  if (!fs.existsSync(claudeMdPath)) {
+    // Create new file with just the CodeGraph section
+    fs.writeFileSync(claudeMdPath, CLAUDE_MD_TEMPLATE + '\n');
+    return { created: true, updated: false };
+  }
+
+  // Read existing content
+  let content = fs.readFileSync(claudeMdPath, 'utf-8');
+
+  // Check for marked section (from previous installer)
+  if (content.includes(CODEGRAPH_SECTION_START)) {
+    // Replace the marked section
+    const startIdx = content.indexOf(CODEGRAPH_SECTION_START);
+    const endIdx = content.indexOf(CODEGRAPH_SECTION_END);
+
+    if (endIdx > startIdx) {
+      // Replace existing marked section
+      const before = content.substring(0, startIdx);
+      const after = content.substring(endIdx + CODEGRAPH_SECTION_END.length);
+      content = before + CLAUDE_MD_TEMPLATE + after;
+      fs.writeFileSync(claudeMdPath, content);
+      return { created: false, updated: true };
+    }
+  }
+
+  // Check for unmarked "## CodeGraph" section (from manual setup)
+  const codegraphHeaderRegex = /\n## CodeGraph\n/;
+  const match = content.match(codegraphHeaderRegex);
+
+  if (match && match.index !== undefined) {
+    // Find the end of the CodeGraph section (next ## header or end of file)
+    const sectionStart = match.index;
+    const afterSection = content.substring(sectionStart + 1);
+    const nextHeaderMatch = afterSection.match(/\n## [^#]/);
+
+    let sectionEnd: number;
+    if (nextHeaderMatch && nextHeaderMatch.index !== undefined) {
+      sectionEnd = sectionStart + 1 + nextHeaderMatch.index;
+    } else {
+      sectionEnd = content.length;
+    }
+
+    // Replace the section
+    const before = content.substring(0, sectionStart);
+    const after = content.substring(sectionEnd);
+    content = before + '\n' + CLAUDE_MD_TEMPLATE + after;
+    fs.writeFileSync(claudeMdPath, content);
+    return { created: false, updated: true };
+  }
+
+  // No existing section, append to end
+  content = content.trimEnd() + '\n\n' + CLAUDE_MD_TEMPLATE + '\n';
+  fs.writeFileSync(claudeMdPath, content);
+  return { created: false, updated: false };
+}