This is a subtask of #111 and relates to the issue-111-update-command branch.

Steps to reproduce

1. Download an old version of a module to the shared module folder
2. Run bee --site=site_name update

Expected result
Module is updated in current location

Actual result
Module is deleted from shared module folder and installed in the site specific module folder.

The cause of this is using the download_bee_callback which when invoked with the site option will download to the site folder.

I think we should fix this at the same time as #297