Generally delete the theme v0.5.0 Alpha from the themes directory and then install the 0.6.0 Alpha is not properly.
Install the v0.6.0 Alpha overwriting the 0.5.0 Alpha is the thing to do.
But in this moment I don't think that it is your problem, rather from what you say maybe "Package Updates" module should be disabled ?!?
You can find it in Modules > Packaging > Package Updates
Please check it and retry to install v0.6.0 Alpha
If above does not work, we will try together deleting the references in the theme v0.5.0 Alpha from the database and then reinstalling the v0.6.0 Alpha