The metadata storage for direct mode (V3) is this. In directory .git/annex/objects, there is one .map for all annexed file, and one .cache for all files in the working tree. Both are small files, containing only 1 line or a few lines. I have a repo with lots of photos, and this created lots of small files. I believe this will cause many performance issues.

It would be great if these files are packed, maybe also in the git pack files format.

direct mode has been removed. Its replacement, v7 unlocked, does use a sqlite database that packs all the metadata in one place. done --Joey