How can I clone a git annex remote (bare repository) created with the webapp in command line ? My goal is to be able to access the files using an ssh connection.
There is no difference between a repository created using the assistant and one created by hand. So you can just git clone ssh://server/path or git remote add foo ssh://server/path and use it at the command line like any other repository.
git clone ssh://server/path
git remote add foo ssh://server/path
The assistant interoperates perfectly with the command line; you can switch between them at will at any time.