cbook.Transformer and the StripWater plugin can generate files under outdir

- pretty ugly hack...
- new outdir keyword: if set then output files and trajectories will be
  placed under outdir (and not in the same directory where the original
  trajectories lived)
- The path mangling is pretty gruesome and it is not really always clear
  where output will end up. For instance, symbolic links won't work as expected
  because we use realpath() in many instances, which resolves to the original
  file (especially noteworthy for the StripWater plugin where one has fewer
  ways to customize).

  In principle the code *should* be written in such a way that the output
  really ends up in the current directory by default...
Merge branch 'develop' of github.com:orbeckst/GromacsWrapper into develop