Clean up directory structure

[wagneral]

Proposal: find a way to replace the theme/ directory. There should be a better mechanism storing local files with institution specific configuration. IMHO theming sounds like CSS issues only.

[dennmuel]

Just dumping some ideas here:

• keep the themes dir, but add webfrontend theming to it (see Frontend theming #173)
• maybe add folders for php classes and the like
• check for unnecessary files, e.g. "TODO" or everything related to "palma2go" (the latter also still has a wiki page)