This page says direct mode is "deprecated"; but, v6 is not yet official ( https://git-annex.branchable.com/forum/default_repo_version_is_still_563/ )? So, for now, direct mode is the recommended thing to use?

Maybe, mention in the docs that whereis does not actually contact remotes to check they still have the files (unlike drop). Maybe, print the timestamp of the last check?

Some questions about CHECKPRESENT Key: (1) if Key is a URL backend key, should this return true if CHECKURL on the URL would return CHECKURL-CONTENTS? (2) Should the external special remote implementation call GETURLS on the key and return true if CHECKURL would return CHECKURL-CONTENTS for any of the URLs? (3) Calling GETURLS on a URL key returns an empty list; shouldn't it return a one-element list containing the included URL (at least if a CHECKURL call on that URL would return CHECKURL-CONTENTS)?

If a key has a URL by which it can be downloaded from an external special remote, and the remote supports checkurl but not checkpresent, checkpresentkey says the key isn't in the remote; but git annex whereis --key says there is. Maybe it's as intended, checkpresentkey being a plumbing command, but just wanted to note.

It seems that *E backends ignore file extensions longer than four chars: https://git-annex.branchable.com/bugs/file_extensions_of624_chars_ignored_by42E_backends/ Is there some reason for doing it this way?

"Each subdirectory has the name of a key in one of the key-value backends. The file inside also has the name of the key." -- is it necessary for the file inside to also have the name of the key? Repeating the already long key name leads to very long symlink targets. Could the file inside just be 'f.txt' (or whatever the extension is)?

Also, the terms "key" and "name of the key" are used in various places; are these the same thing?

Indeed, this command did the trick! I didn't even think about using fsck because the git annex info was returning 0 references. Thanks a lot!

I think git annex fsck --fast --from $remote will make the local annex relearn all the files the remote has without transferring them.

What exacly is the difference between SETURIPRESENT and SETURLPRESENT?

After doing rmurl to remove the last URL at which a file is available, 'git annex whereis filename' still shows 'web' as having one of the copies. Bug?