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

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+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!
+