Make shell scripts more cross-platform compatible
Clean up javadoc errors
Merge branch 'scripts' into emergent

* scripts:
  Make shell scripts more cross-platform compatible
More javadoc cleanup
Merge branch 'cleanup' into emergent

* cleanup:
  More javadoc cleanup
  Clean up javadoc errors
Setup logging
TT_OPTS
More logging config
Verbosity
Adding port option
Adding relativePath