disabiling all top-level commands except help and run; basic pipeline run commmand functionality (generic only).
currently using .sh for pipeline scripts.
adding top-level maf annotation pipeline script
use bash for pipeline scripts, currently.
formatting
commenting out currently-unused config file handling
use env vars for gidget source root
making subcommand call more robust wrt path.
updating gidget env var utility import.
Merge branch 'feature/automating-maf-annotation' into develop