On my computer, git annex get filename --from web uses wget which does support .netrc, but for some reason git annex fsck filename --from web does not. Instead, I get a message that the content is missing and git annex is "fixing location log" (slightly unrelated question, but is there any way to stop it from doing this? Just because a URL isn't accessible now, doesn't mean it's content is gone permanently).

I do not want to encode my credentials into the URLs (eg. username:password@example.com) because my password changes frequently and I would have to update all of the URLs.

git-annex 6.20180406 and onwards use http-conduit for everything by default. To use the .netrc file, run:

git config annex.web-options --netrc

That will make git-annex use curl for all web accesses, and configures curl to use your netrc file. done --Joey