Setting up a CraftCMS website and plugins with Composer

composer.json

{
    "name": "idcorp/silverado",
    "type": "project",
    "authors": [
        {
            "name": "Derrick Grigg",
            "email": "derrick@dgrigg.com"
        }
    ],
    "minimum-stability": "dev",
    "repositories": [
        {
            "type": "package",
            "package": {
                "name": "craftcms/cms",
                "version": "master",
                "dist": {
                    "type": "zip",
                    "url": "https://craftcms.com/latest.zip?accept_license=yes"
                }

            }
        },
        {
            "url": "https://github.com/Firstborn/Craft-CMS-Migration-Manager.git",
            "type": "git"
        },
        {
            "type": "package",
            "package" : {
                "name" : "verbb/super-table",
                "version" : "master",
                "dist": {
                    "type": "zip",
                    "url": "https://github.com/verbb/super-table/archive/craft-2.zip"
                }
            }

        },
        {
            "type": "package",
            "package" : {
                "name" : "fruitstudios/linkit",
                "version" : "master",
                "dist": {
                    "type": "zip",
                    "url": "https://github.com/fruitstudios/LinkIt/archive/master.zip"
                }
            }

        },
        {
            "type": "package",
            "package" : {
                "name" : "fromtheoutfit/navee",
                "version" : "master",
                "dist": {
                    "type": "zip",
                    "url": "https://github.com/fromtheoutfit/navee/archive/master.zip"
                }
            }
        },
        {
            "type": "package",
            "package" : {
                "name" : "joshuabaker/craft-sitemap",
                "version" : "master",
                "dist": {
                    "type": "zip",
                    "url": "https://github.com/joshuabaker/craft-sitemap/archive/master.zip"
                }
            }

        },
        {
            "type": "package",
            "package" : {
                "name" : "aelvan/imager-craft",
                "version" : "master",
                "dist": {
                    "type": "zip",
                    "url": "https://github.com/aelvan/Imager-Craft/archive/master.zip"
                }
            }
        },
        {
            "url": "https://github.com/dgrigg/knockknock.git",
            "type": "git"
        }
    ],

    "require": {
        "craftcms/cms" : "dev-master",
        "verbb/super-table" : "dev-master",
        "firstborn/craft-cms-migration-manager": "dev-master",
        "nystudio107/seomatic": "dev-master",
        "ryanshrum/hacksaw": "dev-master",
        "fruitstudios/linkit": "dev-master",
        "fromtheoutfit/navee": "dev-master",
        "joshuabaker/craft-sitemap": "dev-master",
        "aelvan/imager-craft": "dev-master",
        "dgrigg/knockknock": "dev-master"
    },
    "scripts": {
        "post-install-cmd": [
            "@php post-install.php"
        ],
        "post-update-cmd": [
            "@php post-install.php"
        ]
    }
}

post-install.php

<?php
/****************************************************************************************************************************
Setup each folder for craft, this is done folder by folder to prevent overwriting changed files during installation.
Craft core files (ie app) should only be installed once, any updates to core files should only happen via the Craft updater
******************************************************************************************************************************/

$craft = [
    [
        'source' => 'vendor/craftcms/cms/craft/app/',
        'destination' => 'craft/app'
    ],
    [
        'source' => 'vendor/craftcms/cms/craft/config/',
        'destination' => 'craft/config'
    ],
    [
        'source' => 'vendor/craftcms/cms/craft/plugins/',
        'destination' => 'craft/plugins'
    ],
    [
        'source' => 'vendor/craftcms/cms/craft/storage/',
        'destination' => 'craft/storage'
    ],
    [
        'source' => 'vendor/craftcms/cms/craft/templates/',
        'destination' => 'craft/templates'
    ],
    [
        'source' => 'vendor/craftcms/cms/public/',
        'destination' => 'public'
    ]
];

$plugins = [
    [
        'source' => 'vendor/firstborn/craft-cms-migration-manager/migrationmanager/',
        'destination' => 'craft/plugins/migrationmanager'
    ],
    [
        'source' => 'vendor/verbb/super-table/supertable/',
        'destination' => 'craft/plugins/supertable'
    ],
    [
        'source' => 'vendor/fruitstudios/linkit/fruitlinkit/',
        'destination' => 'craft/plugins/fruitlinkit'
    ],
    [
        'source' => 'vendor/fromtheoutfit/navee/',
        'destination' => 'craft/plugins/navee'
    ],
    [
        'source' => 'vendor/aelvan/imager-craft/imager/',
        'destination' => 'craft/plugins/imager'
    ]
];

echo 'Install craft' . PHP_EOL;

foreach($craft as $folder) {
    echo 'Installing Craft: ' . $folder['destination'] . PHP_EOL;
    if (is_dir($folder['destination']))
    {
        echo 'Whoops ... ' . $folder['destination'] . ' already exists!' . PHP_EOL;
      } else {
        shell_exec(strtr('rsync -az source destination', $folder));
    }
}

echo 'Install plugins' . PHP_EOL;
foreach($plugins as $plugin) {
    echo 'Installing plugins: ' . $plugin['destination'] . PHP_EOL;
    shell_exec(strtr('rsync -az source destination', $plugin));
}
shell_exec('find craft/plugins | grep .git | xargs rm -rf');