There should be a way to specify additional information for how the script should run. I thought comments in the script could be parsed to specify additional information.
e.g.
#!/usr/bin/env python
specify arguments in JSON
brackets-scriptexec.arguments=[one','two','three']
specify enviroment variables in JSON
brackets-scriptexec.enviroment={var1: 'value1', var2: 'value2'}
specify a directory to start in:
brackets-scriptexec.cwd=/Users/dschaffe/starting_directory