git-annex/doc/bugs/Repo_manipulation_breaks_git-annex_drop_--all.mdwn

I am working with a bare repository to transfer two keys from a custom backend to and from a special remote. This seems to be working fine.

In order to be able to make use of export remotes (exporttree=yes), I need to be able to specific a tree to be exported. For technical reasons, I want to keep using a bare repository, and use a `hash-object`, `update-index`, and `write-tree` manually in order to create a tree. The Python code snippet that does this looks like this:

```
    for key, prefix, fname in (
            # the prefixes are constant hashdir-lower
            (RepoAnnexGitRemote.refs_key, 'a11/1c8', '.datalad/dotgit/refs'),
            (RepoAnnexGitRemote.repo_export_key, '6b2/c13',
             '.datalad/dotgit/repo-export.zip')):
        # create a blob for the annex link
        out = repo._git_runner.run(
            ['git', 'hash-object', '-w', '--stdin'],
            stdin=bytes(
                f'../../.git/annex/objects/{prefix}/{key}/{key}', 'utf-8'),
            protocol=StdOutCapture)
        linkhash = out['stdout'].strip()
        # place link into a tree
        out = repo._git_runner.run(
            ['git', 'update-index', '--add', '--cacheinfo', '120000',
             linkhash, fname],
            protocol=StdOutCapture)
    # write the complete tree, and return ID
    out = repo._git_runner.run(
        ['git', 'write-tree'],
        protocol=StdOutCapture)
    exporttree = out['stdout'].strip()
 ```

It essentially creates the two blobs for the annex links, puts them together in a tree, and writes it to the repo.

However, after this code ran, git-annex is not longer operating properly in the bare repo:

```
% git annex drop --all
fatal: relative path syntax can't be used outside working tree
fatal: relative path syntax can't be used outside working tree
fatal: relative path syntax can't be used outside working tree
fatal: relative path syntax can't be used outside working tree
fatal: relative path syntax can't be used outside working tree
fatal: relative path syntax can't be used outside working tree
fatal: relative path syntax can't be used outside working tree
fatal: relative path syntax can't be used outside working tree
fatal: relative path syntax can't be used outside working tree
fatal: relative path syntax can't be used outside working tree
fatal: relative path syntax can't be used outside working tree
git-annex: fd:21: Data.ByteString.hGetLine: end of file
```

(fatal error messages are from cat-file batch calls inside)

When I comment this code out, everything goes back to normal. It seems to makes no difference whether I follow the problematic code up with a `commit-tree` and `update-ref` to actually have the mainline branch point to a commit with that tree. It also seems to make no difference, when I explicitly `setpresentkey <key> <here> 0`.

AFAICS this creates the same records as if I would have done this in a regular worktree using high-level git-annex tooling. Other git-annex commands like `fsck` seem to be working fine. If a create a branch with that tree, also `findref` seems to be working properly.

Is this a bug, or am I doing something wrong? Thanks in advance for your time!

> [[fixed|done]] --[[Joey]]