Maybe you had a lot of files scattered around on different drives, and you added them all into a single git-annex repository. Some of the files are surely duplicates of others.

While git-annex stores the file contents efficiently, it would still help in cleaning up this mess if you could find, and perhaps remove the duplicate files.

Here's a command line that will show duplicate sets of files grouped together:

git annex find --include '*' --format='${file} ${escaped_key}\n' | \
    sort -k2 | uniq --all-repeated=separate -f1 | \
    sed 's/ [^ ]*$//'

Here's a command line that will remove one of each duplicate set of files:

git annex find --include '*' --format='${file} ${escaped_key}\n' | \
    sort -k2 | uniq --repeated -f1 | sed 's/ [^ ]*$//' | \
    xargs -d '\n' git rm

--Joey