We should revist this. It's mostly for convenience since lots of people just put the m2sh stuff wherever everything else goes. Problem is that screws up virtualenv folks.
It's not so much about Python being fragile, it's more that the OS - Linux in particular - uses Python itself, and modules can modify the behavior and break it. (same things if you used Puppet to manage your configs and broke your OS Ruby).
Keeping everything in one dir also makes deployment way simpler.
From your commit log:
> Disable target install-py for now, it requires sudo.
Agreed: re: disabling app that needs root unnecessarily. I don't want anything fucking with my OS python.
Have you considered having it simply call pip instead, so it installs to the current virtualenv?