Fix silly type mistake.

Bug limited max merge to uchar size.
Factor out file IO.
Add routing table checker.
Expand Xs prior to checking.

- Fixes #3
- Make samples_to_bin/bin_to_samples executable.
Toughen up equivalence check.
Bugfix in building covering terms.
Complete pattern aliasing integration.
Merge branch 'master' into pattern_dict
Modify Makefiles.
Fix silly mistake.