git-clone makes it easy to specify a name other than "origin" via the --origin option, and, as of Git 2.30.0, via the clone.defaultRemoteName configuration option. Running git annex init in a clone on a system where git-annex sets annex.crippledfilesystem leads to a crash due to a hard-coded "refs/remotes/origin".

cd "$(mktemp -d "${TMPDIR:-/tmp}"/ga-XXXXXXX)"  || exit 1

export GIT_CONFIG_PARAMETERS="'annex.crippledfilesystem=true'"

git version
git annex version | head -1

git init -q a
git -C a commit -q --allow-empty -m c0
git -C a annex init

git clone --origin=not-origin a b
git -C b annex init
git version
git-annex version: 8.20210331-g17646b0b3
init  (scanning for unlocked files...)

  Entering an adjusted branch where files are unlocked as this filesystem does not support locked files.

Switched to branch 'adjusted/master(unlocked)'
(recording state in git...)
Cloning into 'b'...
init  (merging not-origin/git-annex into git-annex...)
(scanning for unlocked files...)
fatal: refs/remotes/origin/master: not a valid SHA1

git-annex: git [Param "update-ref",Param "refs/heads/master",Param "refs/remotes/origin/master"] failed
CallStack (from HasCallStack):
  error, called at ./Git/Command.hs:42:17 in main:Git.Command
git-annex: init: 1 failed

Thanks in advance for taking a look.

Update: Before posting, I should have tried to trigger this without overriding annex.crippledfilesystem. Entering an adjusted branch in a is sufficient to trigger this.

fixed --Joey