Re-implemented filter application; removed exclusive boolean flag,
implemented two different filter collections to differentiate between
exclusive and inclusive filters.
Refactored and re-implemented the way filters are declared and applied.
All filters are inclusive, in so much as their enforce() method returns
an inclusive FileIndex. The FileIndex includes files that match the
criteria set forth by the filter. For example, a file name filter with
the input String ".docx" will return a FileIndex containing .docx files. 

To deal with this re-implementation, filters need to be applied
inclusively or exclusively depending on the desired result. To remove
certain files then the desired filters' enforce() methods return a
FileIndex that needs to be subtracted (.remove()) from some
running-filter index. To add certain files, it is necessary to add
(.merge()) the FileIndex from enforce() to the running-filter index.
Updated TestCase1.
Updated FileIndex.java; added methods filterExclusively() and
filterInclusively().
Began implementing OptionsContainer.java, an object that encapsulates
the settings, filters, and options for indexing and duplicate file
detection.