First you need to create a repository at github.com. Alternatively you can create a repo on your own machine if you prefer.

Clone the repository and make sure the master is checked out.

```
git clone github.com/username/newsuper.git
cd newsuper
git checkout master
```

It's best practise to add a README.md and LICENSE.md to your super repo. Both of these files are in markdown format and the README will automatically be presented on github.com.

The README should have the following information on what the purpose of your super repo is, and how to install it.

The LICENSE.md should contain information about what license the repo falls under.

Once you have created the files, add them to git.

```
git add README.md LICENSE.md
```

The .gitignore file contains the files and directories that git should ignore when checking in. This is useful for your development directory so config files don't get included in the repository.

The following files should be included in the .gitignore file

```
site/.htaccess
site/ciniki-sync.php
site/ciniki-rest.php
site/ciniki-json.php
site/ciniki-manage.php
site/ciniki-login.php
site/paypal-ipn.php
site/ciniki-apis.php
site/ciniki-api.ini
site/ciniki-manage.ini
site/phpinfo.php
site/index.php
site/ciniki-code
site/ciniki-cache
site/ciniki-backups
logs/
/ssl
```

Add .gitignore to git:
```
git add .gitignore
```

Setup your development server to point at your checked out super repo directory. It's recommended to setup a separate virtual host and keep a logs directory. It's unnecessary for development, but you can also include a self signed SSL cert if required.

Create your htaccess file. The following is recommended:

```
# Block evil spam bots
# List found on : perishablepress.com/press/2006/01/10/stupid-htaccess-tricks/#sec1
RewriteBase /
RewriteCond %{HTTP_USER_AGENT} ^Anarchie [OR]
RewriteCond %{HTTP_USER_AGENT} ^ASPSeek [OR]
RewriteCond %{HTTP_USER_AGENT} ^attach [OR]
RewriteCond %{HTTP_USER_AGENT} ^autoemailspider [OR]
RewriteCond %{HTTP_USER_AGENT} ^Xaldon\ WebSpider [OR]
RewriteCond %{HTTP_USER_AGENT} ^Xenu [OR]
RewriteCond %{HTTP_USER_AGENT} ^Zeus.*Webster [OR]
RewriteCond %{HTTP_USER_AGENT} ^Zeus
RewriteRule ^.* - [F,L]

# Block access to internal code

Options All -Indexes
RewriteEngine On
# Force redirect to strip www from front of domain names
RewriteCond %{HTTP_HOST} ^www\.(.*)$ [NC]
RewriteRule ^(.*)$ %1/$1 [R=301,L]
# Allow access to artweb themes and cache, everything is considered public
RewriteRule ^ciniki-web-layouts/(.*\.)(css|js|png|eot|ttf|woff|svg)$ ciniki-mods/web/layouts/$1$2 [L]
RewriteRule ^ciniki-web-themes/(.*\.)(css|js|html|png|jpg)$ ciniki-mods/web/themes/$1$2 [L]
RewriteRule ^ciniki-web-cache/(.*\.)(css|js|jpg|gif||png|mp3|ogg|wav)$ ciniki-mods/web/cache/$1$2 [L]
RewriteRule ^ciniki-mail-cache/(.*\.)(pdf|js|jpg|png|mp3|ogg|wav)$ ciniki-mods/mail/cache/$1$2 [L]
RewriteRule ^ciniki-code/(.*\.)(zip|ini)$ ciniki-code/$1$2 [L]
RewriteBase /

AddType text/cache-manifest .manifest

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^manager/(.*)$ ciniki-manage.php [L] # allow all ciniki-manage
RewriteRule ^(manager)$ ciniki-manage.php [L] # allow all ciniki-manage
RewriteRule ^(ciniki-mods/[^\/]*/ui/.*)$ $1 [L] # Allow manage content
RewriteRule ^(ciniki-web-themes/.*)$ $1 [L] # Allow manage-theme content
RewriteRule ^(ciniki-mods/web/layouts/.*)$ $1 [L] # Allow web-layouts content
RewriteRule ^(ciniki-mods/web/themes/.*)$ $1 [L] # Allow web-themes content
RewriteRule ^(ciniki-mods/web/cache/.*\.(css|js|jpg|png|mp3|ogg|wav))$ $1 [L] # Allow web-cache content
RewriteRule ^(ciniki-mods/mail/cache/.*\.(pdf|js|jpg|png|mp3|ogg|wav))$ $1 [L] # Allow mail-cache content
RewriteRule ^(phpinfo|paypal-ipn|ciniki-login|ciniki-sync|ciniki-json|ciniki-rest|index|ciniki-manage|ciniki-iframe|ciniki-apis).php$ $1.php [L] # allow entrance php files
RewriteRule ^([_0-9a-zA-Z-]+/)(.*\.php)$ index.php [L] # Redirect all other php requests to index
RewriteRule . index.php [L] # Redirect all other requests to index

php_value post_max_size 20M
php_value upload_max_filesize 20M
php_value magic_quotes 0
php_flag magic_quotes off
php_value magic_quotes_gpc 0
php_flag magic_quotes_gpc off
```

The following directories should be created inside your super repo:

```
mkdir site
mkdir site/ciniki-backups
mkdir site/ciniki-cache
mkdir site/ciniki-lib
mkdir site/ciniki-mods
mkdir site/ciniki-storage
```

The following directories may need their permissions changes so your web server has write permissions to them. If you are running in production these directories should be set to the web server user instead of making them world writable. World writable is easier in a development environment.

```
chmod a+w site/ciniki-cache
chmod a+w site/ciniki-storage
```

You'll need some base ciniki modules for your super repo. The following modules are required unless you are going to build your own versions of them.

```
git submodule add git://github.com/ciniki/businesses.git site/ciniki-mods/businesses
git submodule add git://github.com/ciniki/bugs.git site/ciniki-mods/bugs
git submodule add git://github.com/ciniki/core.git site/ciniki-mods/core
git submodule add git://github.com/ciniki/images.git site/ciniki-mods/images
git submodule add git://github.com/ciniki/sysadmin.git site/ciniki-mods/sysadmin
git submodule add git://github.com/ciniki/users.git site/ciniki-mods/users
```

Recommended modules:
```
git submodule add git://github.com/ciniki/blog.git site/ciniki-mods/blog
git submodule add git://github.com/ciniki/customers.git site/ciniki-mods/customers
git submodule add git://github.com/ciniki/events.git site/ciniki-mods/events
git submodule add git://github.com/ciniki/gallery.git site/ciniki-mods/gallery
git submodule add git://github.com/ciniki/info.git site/ciniki-mods/info
git submodule add git://github.com/ciniki/links.git site/ciniki-mods/links
git submodule add git://github.com/ciniki/mail.git site/ciniki-mods/mail
git submodule add git://github.com/ciniki/subscriptions.git site/ciniki-mods/subscriptions
git submodule add git://github.com/ciniki/web.git site/ciniki-mods/web
```

The following libraries are required by some modules.

```
git clone git://github.com/Synchro/PHPMailer.git site/ciniki-lib/PHPMailer
git clone git://github.com/PHPOffice/PHPWord.git site/ciniki-lib/PHPWord
git clone git://github.com/PHPOffice/PHPExcel.git site/ciniki-lib/PHPExcel
git clone git://github.com/dropbox/dropbox-sdk-php site/ciniki-lib/dropbox
```

TCPDF will need to be downloaded and extracted into site/ciniki-lib/tcpdf

sourceforge.net/projects/tcpdf/files

One the modules have been added, their script files need to be linked into the root of the site directory:

```
cd site
ln -s ciniki-mods/core/scripts/apis.php ciniki-apis.php
ln -s ciniki-mods/core/scripts/json.php ciniki-json.php
ln -s ciniki-mods/core/scripts/login.php ciniki-login.php
ln -s ciniki-mods/core/scripts/manage.php ciniki-manage.php
ln -s ciniki-mods/core/scripts/rest.php ciniki-rest.php
ln -s ciniki-mods/core/scripts/sync.php ciniki-sync.php
ln -s ciniki-mods/web/scripts/index index.php
ln -s ciniki-mods/core/scripts/paypal-ipn.php paypal-ipn.php
```

The web module requires the web server to have permissions to some files for write.

```
chmod a+w site/ciniki-mods/web/cache
```

Create the commit.sh script. This script will automatically roll up the submodule commit logs and create a super repo commit message with them. An optional message can be added as an argument.

```
#!/bin/sh

#
# This script will commit the submodule changes to the Ciniki super repo
#
if [ $# -eq 0 ]; then
MSG="Module Updates:
"
else
MSG="$1

Module Updates:
"
fi

if [ $# -gt 1 ]
then
echo "Too many arguments, put your message quotes.\n";
exit;
fi

SUMMARY=`git submodule summary`;

echo "$MSG$SUMMARY"
git commit -am "$MSG$SUMMARY"
```

Set the script executable and add the script to git:
```
chmod +x commit.sh
git add commit.sh
```

Commit your submodule additions and changes to the super repo.

```
./commit.sh 'Initial setup of my super repo'
```

Now push the changes to github.com
```
git push
```