Extracted Server Functionality from the eclipse package into new server package.
Created new package for eclipse preference classes.
Renamed ViewModule and ViewApp to ModuleView and AppView, since we already call them that all the time.

The old names where ViewModule and ViewApp to have both classes next to each other in alphabetical order. Now that the eclipse package is smaller / the preference classes from eclipse got their own subpackage, this is no longer needed.
Applied renaming ViewModule and ViewApp and the new preferences package to plugin.xml
Applied new server package to eclipse classes.
Added Class to contain main funcionality of the command line program.
auto-formatted the Function block loader for the command line program. no code changes, still doesn't work due to Class Not Found Exception concerning the Resource class.
Applied new server package to command package, worked on command line program.