docs: Clean up README formatting and remove deprecated CLI hook commands

Removes crystal ball emoji and bullet formatting inconsistencies from README headers. Eliminates mark-dirty and sync-if-dirty CLI commands and related hook configuration code, simplifying the codebase after transitioning to file watcher-based auto-sync.

src/installer/config-writer.ts

@@ -192,94 +192,6 @@ export function hasPermissions(location: InstallLocation): boolean {
   return permissions.some((p: string) => p.startsWith('mcp__codegraph__'));
 }
 
-// =============================================================================
-// Hooks Configuration
-// =============================================================================
-
-/**
- * Get the hooks configuration for Claude Code auto-sync.
- *
- * PostToolUse(Edit|Write) → mark-dirty (async, non-blocking)
- * Stop → sync-if-dirty (sync, ensures fresh index before next user turn)
- */
-function getHooksConfig(): Record<string, any> {
-  const command = 'codegraph';
-
-  return {
-    PostToolUse: [
-      {
-        matcher: 'Edit|Write',
-        hooks: [
-          {
-            type: 'command',
-            command: `${command} mark-dirty`,
-            async: true,
-          },
-        ],
-      },
-    ],
-    Stop: [
-      {
-        matcher: '.*',
-        hooks: [
-          {
-            type: 'command',
-            command: `${command} sync-if-dirty`,
-          },
-        ],
-      },
-    ],
-  };
-}
-
-/**
- * Check if Claude Code hooks already exist for CodeGraph
- */
-export function hasHooks(location: InstallLocation): boolean {
-  const settingsPath = getSettingsJsonPath(location);
-  const settings = readJsonFile(settingsPath);
-  const hooks = settings.hooks;
-  if (!hooks) return false;
-
-  // Check if any hook command references codegraph
-  const json = JSON.stringify(hooks);
-  return json.includes('codegraph mark-dirty') || json.includes('codegraph sync-if-dirty');
-}
-
-/**
- * Write Claude Code hooks to settings.json for auto-sync.
- * Merges with existing hooks, deduplicating any previous codegraph entries.
- */
-export function writeHooks(location: InstallLocation): void {
-  const settingsPath = getSettingsJsonPath(location);
-  const settings = readJsonFile(settingsPath);
-
-  if (!settings.hooks) {
-    settings.hooks = {};
-  }
-
-  const newHooks = getHooksConfig();
-
-  // For each hook event (PostToolUse, Stop), merge with existing entries
-  for (const [event, newEntries] of Object.entries(newHooks)) {
-    if (!Array.isArray(settings.hooks[event])) {
-      settings.hooks[event] = [];
-    }
-
-    // Remove any existing codegraph entries for this event
-    settings.hooks[event] = (settings.hooks[event] as any[]).filter((entry: any) => {
-      // Keep entries that don't reference codegraph
-      const entryJson = JSON.stringify(entry);
-      return !entryJson.includes('codegraph mark-dirty') && !entryJson.includes('codegraph sync-if-dirty');
-    });
-
-    // Add new codegraph entries
-    settings.hooks[event].push(...(newEntries as any[]));
-  }
-
-  writeJsonFile(settingsPath, settings);
-}
-
 /**
  * Get the path to CLAUDE.md
  * - Global: ~/.claude/CLAUDE.md

src/installer/index.ts

@@ -8,8 +8,8 @@ import { execSync } from 'child_process';
 import * as path from 'path';
 import * as fs from 'fs';
 import {
-  writeMcpConfig, writePermissions, writeClaudeMd, writeHooks,
-  hasMcpConfig, hasPermissions, hasHooks,
+  writeMcpConfig, writePermissions, writeClaudeMd,
+  hasMcpConfig, hasPermissions,
 } from './config-writer';
 
 import type { InstallLocation } from './config-writer';
@@ -50,7 +50,7 @@ export async function runInstaller(): Promise<void> {
 
   // Step 1: Install globally
   const shouldInstallGlobally = await clack.confirm({
-    message: 'Install codegraph globally? (Required for hooks & MCP server)',
+    message: 'Install codegraph globally? (Required for MCP server)',
     initialValue: true,
   });
 
@@ -70,7 +70,7 @@ export async function runInstaller(): Promise<void> {
       clack.log.warn('Try: sudo npm install -g @colbymchenry/codegraph');
     }
   } else {
-    clack.log.info('Skipped global install — hooks and MCP server may not work without it');
+    clack.log.info('Skipped global install — MCP server may not work without it');
   }
 
   // Step 2: Installation location
@@ -140,11 +140,6 @@ function writeConfigs(
     clack.log.success(`${permAction} permissions in ${locationLabel}/settings.json`);
   }
 
-  // Hooks
-  const hookAction = hasHooks(location) ? 'Updated' : 'Added';
-  writeHooks(location);
-  clack.log.success(`${hookAction} auto-sync hooks in ${locationLabel}/settings.json`);
-
   // CLAUDE.md
   const claudeMdResult = writeClaudeMd(location);
   const claudeMdPath = `${locationLabel}/CLAUDE.md`;