Further incorporation of wmf replacement(#31)

This now successfully replaces the file extension in the TEI XML.

- [x] replace wmf with png equivalent
- [ ] test cases for XML replace
- [ ] call to LibreOffice/ImageMagick to convert the file (waiting on upstream?)
Further work on wmf replacement(#31)
Add tests for WMF files

Fixes #31
Major changes to docopt structure

The new docopt structure is much more clear, with less repetition. Instead of the myriad of options, we now use a far more simple [options] to avoid repetition.

I have also implemented an option to let us point the classifier at a pre-extracted document. This is useful for our Zotero test and also fixes #39.
Further re-working of infrastructure

Implemented Debuggable class from which all infrastructure that debugs should derive
Better handling for new option to specify pre-unpacked folder
Remove useless debug statements
Initialize debugger earlier

Debugger is now the first thing to be initialized so that we can log errors in the settings file configuration etc.
Start of Zotero parsing (#2)
Remove old tools directory
Update README file to reflect new command-line structure
Update README
Serialize Zotero objects into a list for future linking {#2)
Drop Zotero objects after saving serialization {#2)
Test case for basic Zotero reference (#2)
Remove footnote duplication error
Handle JSON serialized Zotero elements (#2)
Second Zotero test document for JSON fields (#2)
Footnote tests and numbering

Switched footnote numbering to use generate-id(). Updated tests to reflect change.
Make debug conditional
Fix to Zotero tests