Modify architecture diagram. Add Smith-Waterman alignment diagram.

Signed-off-by: Matthew Heon <matthew.heon@gmail.com>
Relicense to CDDL 1.0

Signed-off-by: Matthew Heon <matthew.heon@gmail.com>
Merge branch 'license'
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