Fix $app connection in Register Method

Register method failed to get a copy of the Application for all uses.
Task:MediaCore Including a new file to keep corejs media file changes, and including it and its dependencies in behavior.php TODO: Implement jQuery version in that file
Task:Core implementing mootools dependency removed core.js as a new file core-jquery-uncompressed.js
Modified functions: Joomla.renderMessages, Joomla.removeMessages
Task:Core Removed new JS file for the jQuery version of core.js and replacing the core-uncompressed.js with jQuery version, Fixing "Joomla" object not found error
Task:Core Including the compressed version of core.js and improving js code style
Two factor authentication plugin using YubiKey

With this plugin you can use a YubiKey hardware token device (available from Yubico.com) for two-factor authentication in Joomla!. The OTP validation is performed against the YubiCloud servers.
SQL files for the YubiKey two factor auth plugin
Changed description of plg_twofactorauth_yubikey for greater clarity
Merge branch 'refs/heads/projects-master' into feature-twofactor-yubikey
Task:Core Adding new line ending and convert to unix line delimiters
Task:Core Fix issue with invalid characters in validation message
Merge branch 'refs/heads/projects-master' into feature-twofactor-yubikey

Conflicts:
	administrator/components/com_admin/sql/updates/mysql/3.2.0.sql
	administrator/components/com_admin/sql/updates/postgresql/3.2.0.sql
Improved YubiKey handling

- Error message shown when you try to activate this feature but the OTP is invalid or doesn't validate against YubiCloud's servers
- Shuffle the list of YubiCloud servers, using a different, random one every time (helps spread out the load and improve the resilience of the implementation)
- Use a time based nonce instead of the form token to prevent YubiCloud responding with REPLAYED_OTP if the form token doesn't change between subsequent attempts
Update assets on upgrate
The YubiKey authentication would always return false
CS update
Merge pull request #96 from dbhurley/assetupdate

CS update
TinyMCE updated to version 4.0.8
Version in XML updated
[#32327] Installation halts at 1st step on PHP 5.3.3. Fix #2297