whitespace
extract method, site_dirs, for easier testing
extract method, site_pkg, for easier testing
extract BEGIN block into import for testing
check for filename in Can't locate errors

Check for filename in "Can't locate" errors since they could be "Can't
locate" some dependency of the site module.
add test coverage for Genome::Site
add test to ensure `gmt lims` is run
simplify execute

Simplify the execute:

- Any non-zero exit code returns false.
- Allow system to deal with escaping arguments.
Merge branch 'AR-126'

We had a couple bugs make it to production due to poor error handling and poor
test coverage.  This branch tries to improve that a bit.