Initial restructuring of Mokuji core.
Fixing backend environment.
Merge branch 'master' into core-restructure
Epic folder moving going on.
URL parser 2 stronk though.
Made Initializer prettier, fixed URL class, removed other index.php files.
A little cleaning up.
Corrected namespace in apidocs.
Merge branch 'master' into core-restructure

Conflicts:
	init.php (solved in mokuji/system/dependencies/init/Tasks.php)
Fixed installing problems.
Extended autoloader to include component classes.
+ Regenerated API docs.
+ Removed many BaseDBUpdates loading statement.
Minor tweak in logo hiding.
Working on an upgrade script for the core rework.
Merge branch 'master' into core-restructure
Started implementing file transfer actions.
Completed this version of the file transfers and package upgrading.
Added alternative detection method for Adapt Albatros, for when changing branches.
Added some files that were missing after the folder structure moving.
Further implemented CoreUpdates.
 * Fixed folder permission bug in io.php.
 * Moved environment constants to environment class.
 * Created file reference checking step.
Fixed file handling dirs problem.
Fixed error displaying bug.