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
Task:Core Adding new line ending and convert to unix line delimiters
Task:Core Fix issue with invalid characters in validation message
Update behavior.php

Second parameter in [script] function should be now [false] for [tabstate] function. This is because this tabs-state.js requires JQuery not full Mootools framework. Setting this to [true] not only load Mootools when it is not required but also cause some conflicts if websites that depends on JQuery without noConflict.
Update joomla.php

Fixes tracker issue: http://joomlacode.org/gf/project/joomla/tracker/?action=TrackerItemEdit&tracker_item_id=32775&start=0
Missing required second argument in array_diff

The $whiteListAttributes variable is missing on the comparison function. 
This pr corrects previous https://github.com/joomla/joomla-cms/pull/2575
Update README.md

I changed some links to J3.1 documentation into J3.2 links (or 3.x links)
Merge pull request #2588 from pe7er/patch-7

Update README.md
 # [#32605] Heading TOO BIG in the screen "Template Manager: Customise
Template"
 # [#32812] *Wrong JText causes double string use
(Fix #2593)
 # [#32815] Issues with the cache permissions  Thanks Tobias Zulauf
(Fix #2597)
 # [#32810] *mod_feed does not render hyperlinks in RSS 2.0 feeds
containing GUIDs + others  Thanks Lewis Rosenthal
(Fix #2600)
 # [#32772] A Header is missing for the beez3 login form.  Thanks Tobias
Zulauf
(Fix #2568)
Remove extra space to fix Jenkins
 # [#32700] Cleanup beez3 error.php
 # [#32675] Missing check in JApplicationSite causes a fatal error
Thanks Michael Babker
(Fix #2584)