ComposerでインストールしたCakePHPからプロジェクトを生成して、CAKE_CORE_INCLUDE_PATHの相対パス化とautoloaderの読込み。

bake-composer.sh

#!/usr/bin/env bash

Vendor/bin/cake bake project --empty -v app

# replace include_path
replace="s/define('CAKE_CORE_INCLUDE_PATH',.*$/define('CAKE_CORE_INCLUDE_PATH', ROOT . DS . 'Vendor' . DS . 'cakephp' . DS . 'cakephp' . DS . 'lib');/"

sed -i .orig -e "$replace" app/webroot/index.php app/webroot/test.php

## # replace console path, if CakePHP < 2.5
## replace="s/ini_set('include_path',.*$/ini_set('include_path', \$root . PATH_SEPARATOR .  \$root . \$ds . 'Vendor' . \$ds . 'cakephp' . \$ds . 'cakephp' . \$ds . 'lib' . PATH_SEPARATOR . ini_get('include_path'));/"
## 
## sed -i .orig -e "$replace" app/Console/cake.php

# load composer autoloader in bootstrap.php
cat <<EOT >> app/Config/bootstrap.php

// Load composer autoload.
require ROOT . '/Vendor/autoload.php';

// Remove and re-prepend CakePHP's autoloader as composer thinks it is the most important.
// See https://github.com/composer/composer/commit/c80cb76b9b5082ecc3e5b53b1050f76bb27b127b
spl_autoload_unregister(array('App', 'load'));
spl_autoload_register(array('App', 'load'), true, true);
EOT

# set permission
chmod -R o+w app/tmp/

composer.json

{
    "name": "your_vendor/your_project",
    "require": {
        "cakephp/cakephp": "~2.6.1",
        "composer/installers": "*",
        "cakephp/debug_kit": "2.2.*",
        "cakedc/migrations": "*",
        "cakedc/search": "*",
        "cakedc/utils": "*",
        "cakedc/users": "*"
    },
    "require-dev": {
        "phpunit/phpunit": "~3.7"
    },
    "config": {
        "vendor-dir": "Vendor/"
    },
    "extra": {
        "installer-paths": {
            "plugins/{$name}/": ["type:cakephp-plugin"]
        }
    }
}

consoleスクリプトのパスを書き換え忘れてた。

CakePHPの本体がPackagistに登録されたのでパス等々の修正