refactored command-line interface

- CLI is now completely in file cli.py
- process is now done in cli.getOptions()
  * addition of step-specific arguments
  * parsing
  * addition of constants
  * checking of constraints
- version information is now printed to stdout (fixes issue #9)
strengthened running of bash command during preparation

- xsltproc and astyle now now get input and output via Python mechanisms (no waiting for subprocess left this way)
- preparation 'featurelocations' now deletes comments as they broke identification of feature constants
- preparation 'pretty' does not delete comments and empty lines now to preserve the main style of the source files
- added some TODO tasks