Improved specification of modules directory.

Flux now looks for a modules directory in the following locations:
1. A modules directory in the current working directory
2. A modules directory in the same directory as the metafacture-core jar
   file
3. If the first commandline argument is -modules=PATH, this is used as
   the modules directory
Merge pull request #72 from cboehme/specify-modules-dir

Improved specification of modules directory.