Major updates to literature review.

Ditch old lit review save the N-Gram Filtering chapter. Complete about half of
the sections of the new lit review (still much work to be done. Add missing
cross references to lit review chapters in the Approach section.

Enable hyperlinks - ToC, citations, and cross references are now hyperlinks when
generating PDF output.

Signed-off-by: Matthew Heon <mheon@redhat.com>
Merge branch 'master' into approach
Add Smith-Waterman local alignment figure to lit review

Signed-off-by: Matthew Heon <mheon@redhat.com>
Add definition of academic dishonesty to lit review.

Fix a few cross refs that were missing in methodology.

Signed-off-by: Matthew Heon <matthew.heon@gmail.com>
Further progress on lit review

Signed-off-by: Matthew Heon <mheon@redhat.com>
Further work on lit review; nearly complete first draft

Signed-off-by: Matthew Heon <matthew.heon@gmail.com>
Bump version to 1.0.1

Signed-off-by: Matthew Heon <matthew.heon@gmail.com>