diff --git a/src/ccs.ts b/src/ccs.ts
index 5150ff00..cf11ea69 100644
--- a/src/ccs.ts
+++ b/src/ccs.ts
@@ -15,7 +15,7 @@ import {
 import { getGlobalEnvConfig } from './config/unified-config-loader';
 import { ensureProfileHooks as ensureImageAnalyzerHooks } from './utils/hooks/image-analyzer-profile-hook-injector';
 import { getImageAnalysisHookEnv } from './utils/hooks';
-import { fail, info } from './utils/ui';
+import { fail, info, warn } from './utils/ui';
 
 // Import centralized error handling
 import { handleError, runCleanup } from './errors';
@@ -259,7 +259,6 @@ async function showCachedUpdateNotification(): Promise<boolean> {
 
 async function main(): Promise<void> {
   const args = process.argv.slice(2);
-  const firstArg = args[0];
 
   // Initialize UI colors early to ensure consistent colored output
   // Must happen before any status messages (ok, info, fail, etc.)
@@ -268,6 +267,55 @@ async function main(): Promise<void> {
     await initUI();
   }
 
+  // Parse --config-dir flag (must happen before any config loading)
+  const configDirIdx = args.findIndex((a) => a === '--config-dir' || a.startsWith('--config-dir='));
+  if (configDirIdx !== -1) {
+    const arg = args[configDirIdx];
+    let configDirValue: string | undefined;
+    let spliceCount = 1;
+
+    if (arg.startsWith('--config-dir=')) {
+      configDirValue = arg.split('=').slice(1).join('=');
+    } else {
+      configDirValue = args[configDirIdx + 1];
+      spliceCount = 2;
+    }
+
+    if (!configDirValue || configDirValue.startsWith('-')) {
+      console.error(fail('--config-dir requires a path argument'));
+      process.exit(1);
+    }
+
+    if (!fs.existsSync(configDirValue)) {
+      console.error(fail(`Config directory not found: ${configDirValue}`));
+      console.error(info('Create the directory first, then copy your config files into it.'));
+      process.exit(1);
+    }
+
+    const { setGlobalConfigDir, detectCloudSyncPath } = await import('./utils/config-manager');
+    setGlobalConfigDir(configDirValue);
+
+    // Security warning: cloud sync paths expose OAuth tokens
+    const cloudService = detectCloudSyncPath(configDirValue);
+    if (cloudService) {
+      console.error(warn(`CCS directory is under ${cloudService}.`));
+      console.error('    OAuth tokens in cliproxy/auth/ will be synced to cloud.');
+    }
+
+    // Remove consumed args so they don't leak to Claude CLI
+    args.splice(configDirIdx, spliceCount);
+  } else if (process.env.CCS_DIR) {
+    // Also warn for CCS_DIR env var pointing to cloud sync
+    const { detectCloudSyncPath } = await import('./utils/config-manager');
+    const cloudService = detectCloudSyncPath(process.env.CCS_DIR);
+    if (cloudService) {
+      console.error(warn(`CCS directory is under ${cloudService}.`));
+      console.error('    OAuth tokens in cliproxy/auth/ will be synced to cloud.');
+    }
+  }
+
+  const firstArg = args[0];
+
   // Trigger update check early for ALL commands except version/help/update
   // Only if TTY and not CI to avoid noise in automated environments
   const skipUpdateCheck = [
diff --git a/src/commands/help-command.ts b/src/commands/help-command.ts
index 2097453f..4f2c1d59 100644
--- a/src/commands/help-command.ts
+++ b/src/commands/help-command.ts
@@ -2,6 +2,7 @@ import * as fs from 'fs';
 import * as path from 'path';
 import { initUI, box, color, dim, sectionHeader, subheader } from '../utils/ui';
 import { isUnifiedMode } from '../config/unified-config-loader';
+import { getCcsDir, getCcsDirSource } from '../utils/config-manager';
 
 // Get version from package.json (same as version-command.ts)
 const VERSION = JSON.parse(
@@ -259,17 +260,20 @@ Run ${color('ccs config', 'command')} for web dashboard`.trim();
 
   // Flags
   printSubSection('Flags', [
+    ['--config-dir <path>', 'Use custom CCS config directory'],
     ['-h, --help', 'Show this help message'],
     ['-v, --version', 'Show version and installation info'],
     ['-sc, --shell-completion', 'Install shell auto-completion'],
   ]);
 
   // Configuration
+  const [dirSource] = getCcsDirSource();
+  const dirDisplay = dirSource === 'default' ? '~/.ccs' : getCcsDir();
   printConfigSection('Configuration', [
-    ['Config File:', isUnifiedMode() ? '~/.ccs/config.yaml' : '~/.ccs/config.json'],
-    ['Profiles:', '~/.ccs/profiles.json'],
-    ['Instances:', '~/.ccs/instances/'],
-    ['Settings:', '~/.ccs/*.settings.json'],
+    ['Config File:', isUnifiedMode() ? `${dirDisplay}/config.yaml` : `${dirDisplay}/config.json`],
+    ['Profiles:', `${dirDisplay}/profiles.json`],
+    ['Instances:', `${dirDisplay}/instances/`],
+    ['Settings:', `${dirDisplay}/*.settings.json`],
   ]);
 
   // CLI Proxy management
@@ -336,6 +340,13 @@ Run ${color('ccs config', 'command')} for web dashboard`.trim();
     ['', 'providers (agy, gemini, codex, kiro, ghcp).'],
   ]);
 
+  // CCS Environment Variables
+  printSubSection('Environment Variables', [
+    ['CCS_DIR', 'Override CCS config directory (default: ~/.ccs)'],
+    ['CCS_HOME', 'Override home directory (legacy, appends .ccs)'],
+    ['CCS_DEBUG', 'Enable debug logging'],
+  ]);
+
   // CLI Proxy env vars
   printSubSection('CLI Proxy Environment Variables', [
     ['CCS_PROXY_HOST', 'Remote proxy hostname'],
@@ -349,17 +360,17 @@ Run ${color('ccs config', 'command')} for web dashboard`.trim();
 
   // CLI Proxy paths
   console.log(subheader('CLI Proxy:'));
-  console.log(`  Binary:      ${color('~/.ccs/cliproxy/bin/cli-proxy-api-plus', 'path')}`);
-  console.log(`  Config:      ${color('~/.ccs/cliproxy/config.yaml', 'path')}`);
-  console.log(`  Auth:        ${color('~/.ccs/cliproxy/auth/', 'path')}`);
+  console.log(`  Binary:      ${color(`${dirDisplay}/cliproxy/bin/cli-proxy-api-plus`, 'path')}`);
+  console.log(`  Config:      ${color(`${dirDisplay}/cliproxy/config.yaml`, 'path')}`);
+  console.log(`  Auth:        ${color(`${dirDisplay}/cliproxy/auth/`, 'path')}`);
   console.log(`  ${dim('Port: 8317 (default)')}`);
   console.log('');
 
   // Shared Data
   console.log(subheader('Shared Data:'));
-  console.log(`  Commands:    ${color('~/.ccs/shared/commands/', 'path')}`);
-  console.log(`  Skills:      ${color('~/.ccs/shared/skills/', 'path')}`);
-  console.log(`  Agents:      ${color('~/.ccs/shared/agents/', 'path')}`);
+  console.log(`  Commands:    ${color(`${dirDisplay}/shared/commands/`, 'path')}`);
+  console.log(`  Skills:      ${color(`${dirDisplay}/shared/skills/`, 'path')}`);
+  console.log(`  Agents:      ${color(`${dirDisplay}/shared/agents/`, 'path')}`);
   console.log(`  ${dim('Note: Symlinked across all profiles')}`);
   console.log('');
 
diff --git a/src/management/checks/env-check.ts b/src/management/checks/env-check.ts
index c586b07a..95a34a61 100644
--- a/src/management/checks/env-check.ts
+++ b/src/management/checks/env-check.ts
@@ -4,6 +4,7 @@
 
 import { getEnvironmentDiagnostics } from '../environment-diagnostics';
 import { ok, warn } from '../../utils/ui';
+import { getCcsDir, getCcsDirSource } from '../../utils/config-manager';
 import { HealthCheck, IHealthChecker, createSpinner } from './types';
 
 const ora = createSpinner();
@@ -54,6 +55,12 @@ export class EnvironmentChecker implements IHealthChecker {
     }
     console.log(`  ${''.padEnd(24)}  Browser: ${diag.browserReason}`);
 
+    // Show CCS directory and source
+    const ccsDir = getCcsDir();
+    const [dirSource] = getCcsDirSource();
+    const sourceLabel = dirSource === 'default' ? '' : ` (via ${dirSource})`;
+    console.log(`  ${''.padEnd(24)}  CCS Dir: ${ccsDir}${sourceLabel}`);
+
     results.addCheck(
       'Environment',
       envStatus === 'OK' ? 'success' : 'warning',
diff --git a/src/utils/config-manager.ts b/src/utils/config-manager.ts
index 655f5b30..ff8c6b6b 100644
--- a/src/utils/config-manager.ts
+++ b/src/utils/config-manager.ts
@@ -10,6 +10,18 @@ import { isUnifiedMode, loadOrCreateUnifiedConfig } from '../config/unified-conf
 // const { ErrorManager } = require('./error-manager');
 // const RecoveryManager = require('./recovery-manager');
 
+// Module-level state for --config-dir CLI flag override
+let _globalConfigDir: string | undefined;
+
+/**
+ * Set global config directory from --config-dir CLI flag.
+ * Must be called before any config loading.
+ * Pass undefined to clear (useful for tests).
+ */
+export function setGlobalConfigDir(dir: string | undefined): void {
+  _globalConfigDir = dir ? path.resolve(dir) : undefined;
+}
+
 /**
  * Get the CCS home directory (respects CCS_HOME env var for test isolation)
  * @returns Home directory path
@@ -19,11 +31,54 @@ export function getCcsHome(): string {
 }
 
 /**
- * Get the CCS directory path (~/.ccs)
- * @returns Path to .ccs directory
+ * Get the CCS directory path.
+ * Precedence: --config-dir flag > CCS_DIR env > CCS_HOME env (legacy, appends .ccs) > ~/.ccs default
+ * @returns Path to CCS config directory
  */
 export function getCcsDir(): string {
-  return path.join(getCcsHome(), '.ccs');
+  if (_globalConfigDir) return _globalConfigDir;
+  if (process.env.CCS_DIR) return path.resolve(process.env.CCS_DIR);
+  if (process.env.CCS_HOME) return path.join(process.env.CCS_HOME, '.ccs');
+  return path.join(os.homedir(), '.ccs');
+}
+
+/**
+ * Get which source determined the CCS directory (for diagnostics).
+ * @returns [source_label, resolved_path] tuple
+ */
+export function getCcsDirSource(): [string, string] {
+  if (_globalConfigDir) return ['--config-dir', _globalConfigDir];
+  if (process.env.CCS_DIR) return ['CCS_DIR', path.resolve(process.env.CCS_DIR)];
+  if (process.env.CCS_HOME) return ['CCS_HOME', path.join(process.env.CCS_HOME, '.ccs')];
+  return ['default', path.join(os.homedir(), '.ccs')];
+}
+
+/**
+ * Cloud sync folder patterns for security warning.
+ */
+const CLOUD_SYNC_PATTERNS = [
+  'Dropbox',
+  'OneDrive',
+  'Google Drive',
+  'iCloud Drive',
+  'iCloudDrive',
+  'pCloud',
+  'MEGA',
+  'Box Sync',
+];
+
+/**
+ * Check if a path is under a cloud-synced folder.
+ * @returns Detected service name or null
+ */
+export function detectCloudSyncPath(dir: string): string | null {
+  const normalized = dir.replace(/\\/g, '/');
+  for (const pattern of CLOUD_SYNC_PATTERNS) {
+    if (normalized.includes(pattern)) {
+      return pattern;
+    }
+  }
+  return null;
 }
 
 /**
@@ -39,7 +94,7 @@ export function getCcsHooksDir(): string {
  * @deprecated Use getActiveConfigPath() for mode-aware config path
  */
 export function getConfigPath(): string {
-  return process.env.CCS_CONFIG || path.join(getCcsHome(), '.ccs', 'config.json');
+  return process.env.CCS_CONFIG || path.join(getCcsDir(), 'config.json');
 }
 
 /**
diff --git a/tests/unit/config-dir-override.test.js b/tests/unit/config-dir-override.test.js
new file mode 100644
index 00000000..5e075f81
--- /dev/null
+++ b/tests/unit/config-dir-override.test.js
@@ -0,0 +1,113 @@
+/**
+ * Config Directory Override Unit Tests
+ *
+ * Tests CCS_DIR env var and --config-dir flag precedence,
+ * getCcsDirSource() diagnostic, and cloud sync path detection.
+ */
+
+const assert = require('assert');
+const path = require('path');
+const os = require('os');
+
+describe('Config Directory Override', function () {
+  let originalCcsDir;
+  let originalCcsHome;
+
+  beforeEach(function () {
+    originalCcsDir = process.env.CCS_DIR;
+    originalCcsHome = process.env.CCS_HOME;
+    delete process.env.CCS_DIR;
+    delete process.env.CCS_HOME;
+  });
+
+  afterEach(function () {
+    if (originalCcsDir !== undefined) process.env.CCS_DIR = originalCcsDir;
+    else delete process.env.CCS_DIR;
+    if (originalCcsHome !== undefined) process.env.CCS_HOME = originalCcsHome;
+    else delete process.env.CCS_HOME;
+  });
+
+  describe('getCcsDir() precedence', function () {
+    it('should return ~/.ccs by default', function () {
+      const { getCcsDir } = require('../../dist/utils/config-manager');
+      const expected = path.join(os.homedir(), '.ccs');
+      assert.strictEqual(getCcsDir(), expected);
+    });
+
+    it('should use CCS_HOME with .ccs appended (legacy behavior)', function () {
+      process.env.CCS_HOME = '/tmp/test-home';
+      const { getCcsDir } = require('../../dist/utils/config-manager');
+      assert.strictEqual(getCcsDir(), '/tmp/test-home/.ccs');
+    });
+
+    it('should use CCS_DIR directly (no .ccs append)', function () {
+      process.env.CCS_DIR = '/tmp/my-ccs-config';
+      const { getCcsDir } = require('../../dist/utils/config-manager');
+      assert.strictEqual(getCcsDir(), path.resolve('/tmp/my-ccs-config'));
+    });
+
+    it('should give CCS_DIR precedence over CCS_HOME', function () {
+      process.env.CCS_DIR = '/tmp/ccs-dir';
+      process.env.CCS_HOME = '/tmp/ccs-home';
+      const { getCcsDir } = require('../../dist/utils/config-manager');
+      assert.strictEqual(getCcsDir(), path.resolve('/tmp/ccs-dir'));
+    });
+  });
+
+  describe('getCcsDirSource()', function () {
+    it('should return "default" when no overrides set', function () {
+      const { getCcsDirSource } = require('../../dist/utils/config-manager');
+      const [source] = getCcsDirSource();
+      assert.strictEqual(source, 'default');
+    });
+
+    it('should return "CCS_DIR" when CCS_DIR is set', function () {
+      process.env.CCS_DIR = '/tmp/test';
+      const { getCcsDirSource } = require('../../dist/utils/config-manager');
+      const [source] = getCcsDirSource();
+      assert.strictEqual(source, 'CCS_DIR');
+    });
+
+    it('should return "CCS_HOME" when only CCS_HOME is set', function () {
+      process.env.CCS_HOME = '/tmp/home';
+      const { getCcsDirSource } = require('../../dist/utils/config-manager');
+      const [source] = getCcsDirSource();
+      assert.strictEqual(source, 'CCS_HOME');
+    });
+  });
+
+  describe('detectCloudSyncPath()', function () {
+    it('should detect Dropbox', function () {
+      const { detectCloudSyncPath } = require('../../dist/utils/config-manager');
+      assert.strictEqual(detectCloudSyncPath('/Users/kai/Dropbox/ccs'), 'Dropbox');
+    });
+
+    it('should detect OneDrive on Windows paths', function () {
+      const { detectCloudSyncPath } = require('../../dist/utils/config-manager');
+      assert.strictEqual(detectCloudSyncPath('C:\\Users\\kai\\OneDrive\\ccs'), 'OneDrive');
+    });
+
+    it('should detect iCloud Drive', function () {
+      const { detectCloudSyncPath } = require('../../dist/utils/config-manager');
+      assert.strictEqual(
+        detectCloudSyncPath('/Users/kai/Library/Mobile Documents/iCloud Drive/ccs'),
+        'iCloud Drive'
+      );
+    });
+
+    it('should detect Google Drive', function () {
+      const { detectCloudSyncPath } = require('../../dist/utils/config-manager');
+      assert.strictEqual(detectCloudSyncPath('/Users/kai/Google Drive/ccs'), 'Google Drive');
+    });
+
+    it('should return null for regular paths', function () {
+      const { detectCloudSyncPath } = require('../../dist/utils/config-manager');
+      assert.strictEqual(detectCloudSyncPath('/home/kai/.ccs'), null);
+    });
+
+    it('should return null for default ~/.ccs path', function () {
+      const { detectCloudSyncPath } = require('../../dist/utils/config-manager');
+      assert.strictEqual(detectCloudSyncPath(path.join(os.homedir(), '.ccs')), null);
+    });
+  });
+});