In any case, I'll definitely be filing a radar next time it happens. Problem is, it's next to impossible get a repro the problem given the number of variables (environment, SCM, project, the file itself, and whatever UI actions/history that led up to that point), so we come back to the strange fact that only certain projects seem to be affected.
In hard to reproduce cases like this, often the easiest way to get a handle on them is to have Shark sit in the background running a 'Time Profile (WTF)' against Xcode while you work, and that'll enable you to grab a session including not just the time in which Xcode is misbehaving, but also the period leading up to that - often critical in figuring out how and even what state the app has gotten itself into.
The overhead of doing this is negligible, and certainly won't impact your normal Xcode work.
For more information you can read up on Time Profiling in the Shark user manual, and specifically Windowed Time Facility (WTF).
A bug report with such a session attached is much more likely to receive attention than simply stating there's a problem. As noted, it's also likely to be more useful than a simple profile or traditional 'sample', and is easier to obtain.
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