Just as git does not scale well with large files, it can also become painful to work with when you have a large number of files. Below are things I have found to minimise the pain.

Using version 4 index files

During operations which affect the index, git writes an entirely new index out to index.lck and then replaces .git/index with it. With a large number of files, this index file can be quite large and take several seconds to write every time you manipulate the index!

This can be mitigated by changing it to version 4 which uses path compression to reduce the filesize:

git update-index --index-version 4

NOTE: The git documentation warns that this version may not be supported by other git implementations like JGit and libgit2.

Personally, I saw a reduction from 516MB to 206MB (40% of original size) and got a much more responsive git!

It may also be worth doing the same to git-annex's index:

GIT_INDEX_FILE=.git/annex/index git update-index --index-version 4

Though I didn't gain as much here with 89MB to 86MB (96% of original size).

Packing

As I have gc disabled:

git config gc.auto 0

so I control when it is run, I ended up with a lot of loose objects which also cause slowness in git. Using

git count-objects

to tell me how many loose objects I have, when I reach a threshold (~25000), I pack those loose objects and clean things up:

git repack -d
git gc
git prune

File count per directory

If it takes a long time to list the files in a directory, naturally, git(-annex) will be affected by this bottleneck.

You can avoid this by keeping the number of files in a directory to between 5000 and 20000 (depends on the filesystem and its settings).

fpart can be a very useful tool to achieve this.

Topics discussing this sort of usage