With submodules=true, using `./x.py fmt` as a git hook makes bootstrap delete all submodules

[RalfJung]

To reproduce, I am in a worktree without .git (i.e., not the "main" worktree). I have a pre-commit hook set up as follows

#!/bin/sh
./x.py fmt || true # ignore failures

Now I change something trivial (e.g. remove a trailing . in some comments) and commit. That does the following

$ git commit -am test
Building bootstrap
    Finished `dev` profile [unoptimized] target(s) in 0.06s
Updating submodule src/tools/cargo
Saved working directory and index state WIP on from-ref: 64e7337be59 more explicitly state the basic rules of working with the obtained raw pointers

After a second or two I get suspicious and hit Ctrl-C. Now it looks like bootstrap has done something with the (previously clean) cargo submodule

$ git status
On branch from-ref
Your branch is up to date with 'ralf/from-ref'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
  (commit or discard the untracked or modified content in submodules)
    modified:   library/core/src/ptr/mod.rs
    modified:   src/tools/cargo (modified content, untracked content)

So let's cd src/tools/cargo and see what's up

$ git status
HEAD detached at 7a6fad098
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
    modified:   .github/ISSUE_TEMPLATE/config.yml
    modified:   .gitignore
    modified:   CONTRIBUTING.md
    modified:   Cargo.lock
    modified:   Cargo.toml
    modified:   LICENSE-APACHE
    modified:   README.md
    modified:   triagebot.toml

Untracked files:
  (use "git add <file>..." to include in what will be committed)
    .editorconfig
    .git-blame-ignore-revs
    .gitattributes
    .github/ISSUE_TEMPLATE/blank_issue.md
    .github/ISSUE_TEMPLATE/bug_report.md
    .github/ISSUE_TEMPLATE/diagnostics.yaml
    .github/ISSUE_TEMPLATE/documentation.yaml
    .github/ISSUE_TEMPLATE/ice.md
    .github/ISSUE_TEMPLATE/ice.yaml
    .github/ISSUE_TEMPLATE/library_tracking_issue.md
    .github/ISSUE_TEMPLATE/regression.md
    .github/ISSUE_TEMPLATE/tracking_issue.md
    .github/pull_request_template.md
    .github/workflows/ci.yml
    .github/workflows/dependencies.yml
    .gitmodules
    .mailmap
    .reuse/
    COPYRIGHT
    INSTALL.md
    LICENSES/
    RELEASES.md
    compiler/
    config.example.toml
    configure
    library/
    rust-bors.toml
    rustfmt.toml
    src/README.md
    src/bootstrap/
    src/ci/
    src/doc/complement-design-faq.md
    src/doc/complement-lang-faq.md
    src/doc/complement-project-faq.md
    src/doc/favicon.inc
    src/doc/footer.inc
    src/doc/full-toc.inc
    src/doc/grammar.md
    src/doc/guide-crates.md
    src/doc/guide-error-handling.md
    src/doc/guide-ffi.md
    src/doc/guide-macros.md
    src/doc/guide-ownership.md
    src/doc/guide-plugins.md
    src/doc/guide-pointers.md
    src/doc/guide-strings.md
    src/doc/guide-tasks.md
    src/doc/guide-testing.md
    src/doc/guide-unsafe.md
    src/doc/guide.md
    src/doc/index.md
    src/doc/intro.md
    src/doc/man/rustc.1
    src/doc/man/rustdoc.1
    src/doc/not_found.md
    src/doc/redirect.inc
    src/doc/reference.md
    src/doc/robots.txt
    src/doc/rust.css
    src/doc/rust.md
    src/doc/rustc/
    src/doc/rustdoc.md
    src/doc/rustdoc/
    src/doc/style-guide/
    src/doc/tutorial.md
    src/doc/unstable-book/
    src/doc/version_info.html.template
    src/etc/CONFIGS.md
    src/etc/cat-and-grep.sh
    src/etc/completions/
    src/etc/cpu-usage-over-time-plot.sh
    src/etc/ctags.rust
    src/etc/dec2flt_table.py
    src/etc/gdb_load_rust_pretty_printers.py
    src/etc/gdb_lookup.py
    src/etc/gdb_providers.py
    src/etc/generate-deriving-span-tests.py
    src/etc/generate-keyword-tests.py
    src/etc/htmldocck.py
    src/etc/indenter
    src/etc/installer/
    src/etc/lldb_batchmode.py
    src/etc/lldb_commands
    src/etc/lldb_lookup.py
    src/etc/lldb_providers.py
    src/etc/natvis/
    src/etc/pre-push.sh
    src/etc/rust-gdb
    src/etc/rust-gdbgui
    src/etc/rust-lldb
    src/etc/rust-windbg.cmd
    src/etc/rust_analyzer_settings.json
    src/etc/rust_types.py
    src/etc/test-float-parse/
    src/etc/third-party/
    src/librustdoc/
    src/rustdoc-json-types/
    src/stage0
    src/tools/
    src/version
    tests/COMPILER_TESTS.md
    tests/assembly/
    tests/auxiliary/
    tests/codegen-units/
    tests/codegen/
    tests/coverage-run-rustdoc/
    tests/coverage/
    tests/crashes/
    tests/debuginfo/
    tests/incremental/
    tests/mir-opt/
    tests/pretty/
    tests/run-make-fulldeps/
    tests/run-make/
    tests/run-pass-valgrind/
    tests/rustdoc-gui/
    tests/rustdoc-js-std/
    tests/rustdoc-js/
    tests/rustdoc-json/
    tests/rustdoc-ui/
    tests/rustdoc/
    tests/ui-fulldeps/
    tests/ui/
    x
    x.ps1
    x.py

no changes added to commit (use "git add" and/or "git commit -a")

Eh... so the added files are rustc files? Why are those being added in src/tools/cargo?
Something is going seriously wrong here.

[onur-ozkan]

I think this only happens with worktrees. I attempted to reproduce it about 25 times without success.

[RalfJung]

Yes indeed, this does not happen in my rustc folder (the main checkout, where .git lives), but it happens in worktree folders.

[RalfJung]

Adding some debug logging, it seems like some truly strange things are happening...

output from cd "/home/r/src/rust/rustc.2/src/tools/cargo" && "git" "rev-parse" "HEAD" is "d402830c8a356332de93761d6996faf5a2ca29ca\n"

This is the HEAD commit of the outer repository!

I think what's happening is that some environment variables are set inside the git hook which overwrite the --git-dir. x.py relies on just setting the working directory to determine which git dir to use, but e.g. GIT_DIR takes precedence over that. I tried setting --git-dir instead of using current_dir and that does seem to help.