E3-308: Remove duplicated entries in .dep files

If you had source-based dependencies and also included a dependency with the REQUIRED variable, then you would end up with repeated lines in the .dep file. This is not technically a problem for require, but it is unæsthetic.

The fix proposed simplifies the generation of the .dep file. It also moves the grep -v include command a bit earlier: that command exists to avoid including "dependencies" from EPICS base. It seems better to explicitly remove those dependencies, as the existing version would technically prevent the ability to install a module called include that anything else depends on.