Thanks for the contribution! I've got a few comments mostly related to style.
Can you also detail what testing you've done for this change?

We prefer imports to be listed in alphabetical order.

I think I'd prefer if the subprocess.call() and sys.exit() are separate statements.

Instead of doing a whole bunch of list operations, then casting to set, then back to list, let's keep this all as a set until the end. We also like to have blank lines around indented blocks. Perhaps something like this?

commands = {entrypoint.name for entrypoint in entrypoints}

for path_dir in os.environ.get('PATH').split(':'):
    path_prefix = '%s/%s-' % (path_dir, RB_MAIN)

    for cmd in glob.glob(path_prefix + '*'):
        commands.add(cmd.replace(path_prefix, ''))

aliases = load_config.get('ALIASES', {})
commands |= aliases.keys()
commands = list(commands)

Regarding separating the sys.exit and subprocess.call - I was copying the style from here.  Would you like this one separated as well?

Is there anything else you need from me?

This is looking pretty solid!

One last thing I noticed--since we have the commands as a set, we should be able to filter common_commands out of it ahead of time. We probably can also skip the cast to list, since sorted should be able to handle it as-is:

common_commands = ['post', 'patch', 'close', 'diff']
other_commands = commands - set(common_commands)

print('\nThe most commonly used commands are:')
for command in common_commands:
    print('  %s' % command)

print ('\nOther commands:')
for command in sorted(other_commands):
    print('  %s' % command)

Ship It!