Error when using SchemaDefRequirement

[jeremiahsavage]

git clone https://github.com/jeremiahsavage/cwl_schemadef.git
cd cwl_schemadef/

with cwltool

(cwl) ubuntu@jeremiah-node001:~/cwl_schemadef$ cwltool --debug transform.cwl transform.json 
/home/ubuntu/.virtualenvs/cwl/bin/cwltool 1.0.20180403145700
Resolved 'transform.cwl' to 'file:///home/ubuntu/cwl_schemadef/transform.cwl'
[workflow transform.cwl] initialized from file:///home/ubuntu/cwl_schemadef/transform.cwl
[workflow transform.cwl] start
[workflow transform.cwl] completed success
Removing intermediate output directory /tmp/tmpIJBOgP
{}
Final process status is success

with the develop branch of bunny:

(cwl) ubuntu@jeremiah-node001:~/cwl_schemadef$ java -jar ~/rabix-cli-1.0.4/lib/rabix-cli.jar transform.cwl transform.json 
[2018-04-12 22:15:50.643] [DEBUG] Config path: /home/ubuntu/rabix-cli-1.0.4/config
[2018-04-12 22:15:50.646] [DEBUG] Configuration directory found localy.
[2018-04-12 22:15:51.881] [ERROR] Error: file:/home/ubuntu/cwl_schemadef/transform.cwl is not a valid app! current node id is null