Cleanup and extend general (file system) path options

The set of options in common.app.framework.options for specifying paths at the filesystem are very much focused on files, while sometimes directories are required instead. Also, recently the PathPair class was introduced. It seems useful to integrate that in option handling instead of having that in every application.

Ideas:

• Cleanup box writing (!950 (merged))
  • Allow writing a Box to a file pointed to by a PathPair.
  • Adopt it in PLCgen for the writers, CIF to mCRL2, CIF simulator, EMF code generation, and SeText generator.
• Cleanup CifWriter usage (!968 (merged))
  • Supply PathPair to CifWriter, and adapt CIF tools.
• Use userPath instead of systemPath for error messages. See also:
  • !950 (comment 2537038)
  • !950 (comment 2537039)
  • !950 (comment 2537040)
  • !950 (comment 2537041)
  • !950 (comment 2537042)
• Don't use result of File.getPath method as a path to present to users.
  • See also !950 (comment 2537040).
  • On 2024-07-11, in develop, this is only used in TwinCatWriter (both in PLCgen and cif2plc) and in CrashReport (but that use is fine).