We removed the bluepymm-megate command, and everything now goes through the 'bluepymm' command.
It now acts a bit like the 'pip' command, with subcommands.
There are three stages:
prepare, run and select
'bluepymm prepare <configfile>' builds the me-combo database from the input files
'bluepymm run <configfile>' takes the database and runs all the combos
'bluepymm select <configfile>' is the megating step
A sample of a config for the new 'run' phase is here:
https://github.com/BlueBrain/BluePyMM/blob/master/bluepymm/tests/examples/simple1/simple1_conf_run.json
The bluepymm command will show an help message if you run it without argument.