Add a new recipe for resequencing

Added recipe.mk file which runs a typical resequencing workflow. Moving
to break up makefiles into smaller, reusable funtional units that can be
included in other makefiles (e.g., chunk.mk).  Updated README.md to
reflect the changes.
Minor markdown formatting
Update README, add circularize.mk information
Minor markdown format fix
Checkpoint

Learning a lot from assembling human.  Some major changes will be coming
along shortly.
Tweaks to the adaptor workflow

- Switch to numeric IDs instead of PacBio IDs to save space.
- Limit hits from daligner to top 200 based on 'score'.
- Get sequences from the DB instead of creating, merging and reading
from a fasta file.
Merge branch '2.3.0' of github.com:PacificBiosciences/smrtmake into 2.3.0
Clean up after ourselves
Remove some failed experiments
Merge remote branch 'upstream/2.3.0' into 2.3.0