a issue: git annex initremote (in particular, adding a key as described in encryption -- git annex initremote my_remote encryption=my_key) seems to iterate over the .git-annex/???/???/*.log files with lstat (tested using strace).

in a 50k key git-annex on a slow disk, this takes quite a while, while not seeming necessary (it's just re-encrypting the shared secret, is it?).

could you verify the observed behavior?

This is due to git commit being called. git commit exposes git's rather innefficient handling of the index; in order to make a commit it has to write a new index file, and it does this by scanning every file in the repository. I think that git generally needs its index file handleing overhauled, particularly to deal with repositories with large numbers of files. git-annex is seems to already be running git commit in its most efficient mode, by specifying exactly what file to commit. done --Joey