Before using git annex, you need to declare that this is a git annex repository

git annex init

Add a file to git annex

git annex add <filename>

To add the content to the server, just adding the file to git annex is not sufficient. You need to do

git annex sync --content

When you clone or pull a repo, only the annex symlinks are downloaded, the files aren't downloaded. To download the annexed file,

git annex get <filename>

git annex sync --content also downloads the annexed files