Renamed 'dir' option to be consistent with other commands.

Renamed 'dir' option to be consistent with other commands.
Don't call 'set_final_options()' in 'run()' anymore -- that's now
  guaranteed to be taken care of for us by the Distribution instance.
Rearranged to bit to allow outsiders (specifically, the 'dist' command)
  to find out what modules we would build:
  - 'find_modules()' renamed to 'find_package_modules()'
  - most of 'build_modules()' abstracted out to 'find_modules()'
  - added 'get_source_files()' (for the 'dist' command to use)
  - drastically simplified 'build_modules()' -- now just a wrapper around
    'find_modules()' and 'build_module()'