Move "PhaseVariants" tool under GMT.

The test does not currently test anything as it points to
non-existent files.
Whitespace.
Remove un-needed constructor.
Remove un-needed comments.
Print command using debug message.
Switch to snake_case so we get hyphenated params instead of mixed-case.
Add note about switching to shellcmd.

If we switch now the test starts failing.
Remove unused includes.
Merge pull request #177 from tmooney/move_phase_variants

Move "PhaseVariants" tool under GMT.