That is what I will be trying to do for those files not managed by git-annex (not that git-annex support is done yet...). However, I don't know yet what the best way to rewrite the history will be and am happy to take any suggestions at this point. filter-branch is something I have used before for splitting repositories, but there may be better ways to reduce history. From a user point of view, the use cases that should be supported by the trimmed history are IMHO: a) "Give me the state of this directory at a point in time up to X days/weeks/months ago" and b) "I want this file as it was Y revisions ago". Everything that does not fit in either a) or b) with user-configured values for X and Y can be pruned.
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