Project's structure reorganisation

[mdziekon]

Currently there's a huge mess, files / directories non related to the source code being placed alongside of all the sources. Stuff like that. This needs to be fixed.

TODO:

• Source code should reside in src/ directory.
• All "datastores" directories should be outside of source directory.
• Get rid of index.php files that were supposed to stop people from snooping on source code. Rely on webservers "doing the right thing" instead (eg. nginx disabling indexing).
• ajax/ & admin/ dirs should be placed in PHP's code storage (somehow)
• All source files should be "per module / per feature" co-located (eg. galaxy view PHP sources should be in the same directory as its template(s))