git seems to have issues with alternates when cycles are present (repo A has B/objects as alternates, B has A/objects as alternates). In such cases, gc and repack might delete objects that are present in only one of the alternates, leading to data loss.

I understand that this is no big use case, and requires manual editing of objects/info/alternates. But for the sake of preventing unneccesary data loss, and since I found no warning regarding alternate cycles in the documentation, it might make sense to handle such cases properly (maybe it's a simple "after finding all alternates directories, remove duplicates"?).

Here is a small test case that adds the object storage of a repository as alternate to itsself. After git repack -adl, all objects are deleted.

rm -rf test_repo &&
mkdir test_repo &&
cd test_repo &&
git init &&
touch a &&
git add a &&
git commit -m "c1" &&
git repack -adl &&
echo $PWD/.git/objects > .git/objects/info/alternates &&
echo ">> re-packing..." &&
git repack -adl &&
echo ">> git fsck..." &&
git fsck


Initialized empty Git repository in /somewhere/test_repo/.git/
[master (root-commit) ab9e123] c1
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 a
Counting objects: 3, done.
Writing objects: 100% (3/3), done.
Total 3 (delta 0), reused 0 (delta 0)
>> re-packing...
Nothing new to pack.
error: refs/heads/master does not point to a valid object!
>> git fsck...
Checking object directories: 100% (256/256), done.
Checking object directories: 100% (256/256), done.
error: HEAD: invalid sha1 pointer 1494ec24356cbbbd66e19f22cef762dd83de7f54
error: refs/heads/master does not point to a valid object!
notice: No default references
missing blob e69de29bb2d1d6434b8b29ae775ad8c2e48c5391

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