Hi,
So I have yet another idea to speed up git annex. For now only for the 2nd pass of git annex sync --content --all.

1. Do a normal (full) git annex sync. For every remote that we synced with, record the commit id of the current tip of the git-annex branch.
   • Record the commit id only if --content --all was specified
   • Record the commit id only if the remote is actually available and every file was sucessfully transfered
2. If any of the remotes doesn't have a commit id recorded, go to 1. Else do a incremental git annex sync: In the 2nd pass of git annex sync --content --all, only look at keys whose location log changed since the last (full or incremental) sync via git diff-tree -r --name-only <lowest recorded commit id of all remotes> git-annex. Again, update the commit id of remotes that we sucessfully synced with.
3. If one of the following happens, remove all recorded commit ids of all remotes, go to 1. Else go to 2.
   • The preferred content expression of us or one of our remotes changed.
   • The preferred content expression of a group changed
   • The group of any repo (not only remotes) changed. This way remotes containing copies=<group>:<numcopies> recheck all keys.

This should be pretty reliable, but please double check. It has to be reliable enough to become the default.