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#706 CIF data-based synthesis: introduce settings class + split application/library

  • Eliminated use of the application framework within the CIF data-based synthesis plugin. The application class, UI command handler class, and options package, still use and depend on the application framework.
  • Introduced a CifDataSynthesisSettings class to hold the settings. Changed the code to use that rather than the options.
  • I tried to do things in separate commits. There are quite a few. I did forgot a few things, that I added in later commits. Also fixed a regression in a later commit. And made some further improvements in later commits. Not sure whether looking at it per commit or just at the end result is best now.
  • The changes are all quite straightforward, I think.
  • Some end-user error messages related to options/settings have changed.
  • There are more steps to come in #706 (closed). This is about the application/library split only.

Addresses #706 (closed)

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