Initial pin of VCS directory includes untracked and ignored files [2.1 regression]

[dra27]

FROM ocaml/opam:debian-12-opam
RUN git clone https://github.com/ocaml/stdlib-shims.git
RUN sudo ln -f /usr/bin/opam-2.2 /usr/bin/opam
RUN rm -rf ~/.opam && opam init --bare -a ~/opam-repository
RUN touch stdlib-shims/stdlib-shims.install stdlib-shims/untracked
RUN opam switch create --empty stdlib-shims
RUN opam pin add stdlib-shims git+file:///home/opam/stdlib-shims -yn
RUN ls -a /home/opam/.opam/stdlib-shims/.opam-switch/sources/stdlib-shims > before
RUN opam update stdlib-shims
RUN ls -a /home/opam/.opam/stdlib-shims/.opam-switch/sources/stdlib-shims > after
RUN grep '\.git\|untracked\|install' before
RUN diff -u before after

Since opam 2.1, the initial copy of the pin directory incorrectly:

• Has no .git folder
• Has copies of stdlib.shims.install (which is in .gitignore) and untracked (which should be an untracked file)

Replacing the opam-2.2 with opam-2.1 tests 2.1 and and removing that and the following line completely tests 2.0.

The first opam update of the VCS sources causes the .git directory to be added and the untracked/ignored files to be removed.

[kit-ty-kate]

I've just hit the same bug when pinning opam itself locally with my local directory containing vendored dependencies in src_ext

[kit-ty-kate]

it's actually a big issue for local projects that have git submodules that have been pulled as this issue makes them fail completely since #6132. However anecdotally (i need to test a bit more), that setup seem to have worked with opam 2.1 but not 2.2