Fixes to Methodology and Bibliography

Fix broken crossreferences in methodology. Fix missing italics.

Ensure that single build targets for docs work alone.

Signed-off-by: Matthew Heon <mheon@redhat.com>
Update Makefile to provide Maven build targets

Previously, invoking make on the root directory would only build the docs. Most
users likely expect that the code will be built as well. This should improve the
user experience for developers slightly.

Signed-off-by: Matthew Heon <mheon@redhat.com>
Move all sections of paper to their own file. Clean up lit review a tad.

Signed-off-by: Matthew Heon <mheon@redhat.com>
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'