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The manage sites dialog updates the enabled state for repos when the OK button is pressed. This is done from the UI thread. If there are a large number of sites being enabled or disabled, this seemingly hangs the UI thread. Perhaps its having to load repositories to change the Enabled state. Need to investigate where the time is being spent here.
Strange, from looking at the repo manager code, setting enablement shouldn't take much time. It causes the preference file to be updated, so there is some minimal local file system I/O.
It's possible that I was experiencing GC or some other random hang. It doesn't happen all the time. Leaving this bug open so I can investigate (post 3.4) the code path here and see if there's anyone who might be loading a repo in the UI thread as a side effect.
I have not seen this problem in the 3.5 stream. Marking "worksforme"