Move file processing methods into File object
Move file processing methods into File object

- It seems like filecheck will be easier to reason about if all of
the file processing stuff happens in the File object. The Groomer
object will now be responsible only for enumerating the files to
be processed.
- Tests won't pass for this commit, but wanted to make the diff
cleaner but committing this before making changes.

CIRCL/PyCIRCLean,Rafiot/PyCIRCLean,Rafiot/PyCIRCLean,CIRCL/PyCIRCLean