Refactor Index

[haszi]

This PR is a minimal refactoring of Index to move its dependencies out of the class and inject them through the constructor.

The changes are:

• move requireIndexing() method out of Index into a global function that receives all its dependencies through parameters
• add a new IndexRepository class that handles all database access for Index, refactor Index to receive an object of this class as a constructor dependency and to pass raw data to it (i.e. data not containing SQL statements)
• add basic indexing test
• fix existing test that uses indexing to use IndexRepository

[haszi]

Possible future improvements:

• push IndexRepository further up the inheritance tree to Format, this will allow all parts of Phd to use the same indexing database (as opposed to creating new instances in multiple places and sometimes not using the same database that was used for indexing)
• rewrite SQL in IndexRepository to use prepared statements and to possibly use one large INSERT INTO statement vs individual ones for each of the 29k+ index rows - Won't do this: all database access takes no longer than 2-3 seconds total for the entire rendering process (indexing + one format)
• remove the global ReaderKeeper (from all classes) and pass the current Reader to Formats as needed - Removed from Index and Generic\XHTML
• move all index database access from Format to IndexRepository

[Girgias]

Did a brief review but I can't spot anything majorly wrong.