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This issue seems to manifest only under this specific case:
Upgrading only MFA from MFA 4.0.4 (stable) to MFA 4.0.6 (beta) using MonoDevelop 18.104.22.168 (beta).
Error pop-up: https://gist.github.com/2228730
kill -QUIT log: https://gist.github.com/2228757
When upgrading *only* MfA, the MD 'Updates are available for MonoDevelop" window does not close when the installer starts.
This allows you to select [Upgrade] again after the installer finishes.
This then throws two errors. Closing those errors and then selecting 'Check for Updates' again gets you into the state shown at the end of the screencast where closing the pop-up simply reopens a new one.
Then MonoDevelop must be force quit to get out of this.
This behavior is *not* exhibited when using the beta MonoDevelop (22.214.171.124) to downgrade from 4.0.6 to 4.0.4
This behavior is *not* exhibited when using the stable MonoDevelop (126.96.36.199) to upgrade from 4.0.4 to 4.0.6
Fixed being able to install the same update again on master, investigating the other issues.
I found a possible cause for the exceptions and fixed it too.
Assuming my fixes worked, since it hasn't been reported again.