update manifest
correct package name
change name of domain-finding command class
update command number
update search to run command for tests
add command class for search pfam for terms
add tests for pfamsearch command
bump version
update changes
bump version
add method to get mapping file without one being supplied
add some file/dir tests
add tests for mapping terms without a user-supplied mapping file
update readme for new commands
make sure var is defined
fix option number
add import for debug
sync branches for build
update deps
remove import used for debug