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Issue #152 exposed a problem with our dirty bit management, which was relying on CodeMirror's undo history. Because CodeMirror limits the size of its undo history, our logic for figuring out when to clear the dirty bit due to an undo was incorrect.
The real fix for this would be to add the dirty bit tracking to CodeMirror. For now, we're simplifying the dirty bit management so that we simply mark documents as dirty as soon as you make a change, and only mark them clean again on save. If you undo back to your previous save state, the document is still marked dirty. This avoids the data loss issue from 152, but is not as good from the user's point of view. We'll add a user story to the product backlog to get back to the previous functionality.