Doc improvement: clarify the process for backing up and migrating configuration and secret keys.

What does this MR do?

Attempts to clarify the steps necessary to migrate configuration and secret keys during a backup and restore process.

Are there points in the code the reviewer needs to double check?

Ensure that I haven't mis-stated anything about how keys are used, etc.

Why was this MR needed?

I performed a migration from source install to Omnibus, following this doc, and ran into authentication issues. It turned out that this was because I did not migrate any of my secret keys. I didn't do that because the doc seemed to say that they would only impact two-factor auth, which we are not using. But in fact I at least needed to migrate my .gitlab_shell_secret key, in order for anyone to be able to push or clone repos.