refactor: deprecate legacy code

[mrossinek]

What is the expected enhancement?

#746 migrated (almost) the entire code base into a new structure.
While doing so, we did not yet add deprecation warnings for the legacy code. This issue can be closed, once all legacy modules have deprecation warnings associated with them.

Some caveats:

• the BOPESSampler-related code has not been migrated. However, it should still be deprecated. A feature request will be opened shortly explaining how we may achieve warm-starting variational algorithms in the future. This will be the de-facto replacement of the BOPESSampler. (EDIT: link to said issue Warm-Starting InitialPoint #750)
• the protein folding code has also not been migrated. Extract the Protein Folding Code #742 reflects that this code will indeed be extracted into another repository in its entirety. Maybe we should hold off with the deprecation warnings on that particular code, until the extraction has been done.