git based registry fails to update

[benlorenz]

I have noticed that some of my github actions jobs are failing to update the general registry and are stuck on an old version, both on 1.13 and 1.14:

┌ Warning: Cannot perform fast-forward merge
└ @ LibGit2 /opt/hostedtoolcache/julia/1.13-nightly/x64/share/julia/stdlib/v1.13/LibGit2/src/merge.jl:241
┌ Error: Some registries failed to update:
│     — /home/runner/.julia/registries/General — registry failed to rebase on origin/master
└ @ Pkg.Registry /opt/hostedtoolcache/julia/1.13-nightly/x64/share/julia/stdlib/v1.13/Pkg/src/Registry/Registry.jl:685

The action is using the julia-cache action to cache some files of the depot, including the registry.
https://github.com/oscar-system/Polymake.jl/actions/runs/20024383358/job/57418291283#step:6:51

To reproduce locally:

Add the general registry via git:

julia> ENV["JULIA_PKG_SERVER"]
""

(@v1.14) pkg> registry add General
     Cloning registry from "https://github.com/JuliaRegistries/General.git"
       Added registry `General` to `~/.julia/registries/General`

shell> git -P -C ~/.julia/registries/General/ log --oneline master origin/master
0b28ba5f7 (grafted, HEAD -> master, origin/master, origin/HEAD) New version: ProteinChains v0.7.5 (#143904)

Now wait until new packages have been merged to the registry.

(@v1.14) pkg> up
    Updating registry at `~/.julia/registries/General`
    Updating git-repo `https://github.com/JuliaRegistries/General.git`
┌ Warning: Cannot perform fast-forward merge
└ @ LibGit2 ~/software/polymake/julia/julia/julia-nightly/share/julia/stdlib/v1.14/LibGit2/src/merge.jl:241
┌ Error: Some registries failed to update:
│     — /home/lorenz/.julia/registries/General — registry failed to rebase on origin/master
└ @ Pkg.Registry ~/software/polymake/julia/julia/julia-nightly/share/julia/stdlib/v1.14/Pkg/src/Registry/Registry.jl:685
     Project No packages added to or removed from `~/.julia/environments/v1.14/Project.toml`
    Manifest No packages added to or removed from `~/.julia/environments/v1.14/Manifest.toml`

shell> git -P -C ~/.julia/registries/General/ log --oneline master origin/master
f0ed5acaa (grafted, origin/master, origin/HEAD) New version: CTBase v0.17.1 (#143905)
0b28ba5f7 (grafted, HEAD -> master) New version: ProteinChains v0.7.5 (#143904)

The new origin/master has been fetched but cannot be merged without any history due to the shallow clone.

Probably related to: #4487