Document that `gt fingerprint` is case insensitive.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Update generated documentation for `gt fingerprint`.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Add unit test to assert `gt fingerprint` is case insensitive.

Data used in this unit test:
- U89959_ests_gi_8690080_soft_masked.fas is gi|8690080 from U89959_ests.fas,
  but arbitrarily soft-masked.
- U89959_ests_gi_8690080_unmasked.checklist is MD5 fingerprint of gi|8690080
  from U89959_ests.fas.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Merge pull request #393 from yeban/fingerprint_is_case_insensitive

Document case insensitive fingerprints. Closes #386.
make LTR clustering accept region mappings, intermediate
intermediate
cosmetics
memleaks
cleanups