I made a couple of changes to IMP module/application structure to to try to make things a bit cleaner before the release.

First, the main documentation page for modules and applications has been moved into a file called README.md in the module/applications main directory (from doc/overview.dox). This file is a markdown file that is then displayed - by github when you browse the directory - provides a natural file for people to look at if they are looking through the source - and, of course, is show by doxygen as the documentation for the module (it is now a separate page rather than being mixed in with the docs for the functions/classes)

I cleaned the files up a bit, but, in general, the contents have been a bit neglected. It might be worth people looking at the files for modules they are associated with to make sure everything is how they want. These changes only effect documentation, so are unlikely to break anything with modules that are not in imp proper.

Second, I renamed the "description" files to "dependencies.py" as they are python files that describe module/application dependencies. If you want backwards compatibility in a module, just rename the file and create a symlink as "description". I updated isd2 and npctransport.