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I have a large git repository with binary files scattered over different branches. I want to switch to git-annex mainly for performance reasons, but I don't want to loose my history.

I tried to rewrite the (cloned) repository with git-filter-branch but failed miserably for several reasons:

* --tree-filter performs its operations in a temporary directory (.git-rewrite/t/) so the symlinks point to the wrong destination (../../.git/annex/).
* annex log files are stored in .git-annex/ instead of .git-rewrite/t/.git-annex/ so the filter operation misses them

Any suggestions how to proceed?