[FIX] fix how swath files are annotated

- fix broken mapping between swath file vector and swath annotation file
  (no MS1 map annotation)
- add checks for correct number of entries in the annotation files
- handle proteowizard converted files which only contain the target m/z
  and no window information
- increase debug output verbosity
Merge pull request #678 from hroest/feature/SWATH_annotation

[FIX] fix how swath files are annotated