add option to specify config file

allows one to have multiple configuration files (json/yml) in same dir
and select which to use via cmdline option
rename Config type to Options, and the variables too

Better name to represent the cmdline options
Cleanup config file handling: rename manifestFiles, fix default

mostly cleanup, but also fixed the defaults to include crane.yml
instead of repeating crane.json twice.
Merge pull request #15 from rliebling/allow_alternate_config_file

Allow option to specify config file