Bootstrap fails to build when switching between submodule and subtree

[jethrogb]

When switching between git trees where one contains clippy as a submodule and one contains clippy in tree, x.py fails to initialize the submodule correctly in some cases, resulting in a failed build. For example:

git clone https://github.com/jethrogb/rust/ -b clippy-submodule
cd rust
./x.py help
git checkout -f clippy-tree
./x.py help
git checkout -f -
./x.py help

error: failed to read `/tmp/rust/src/tools/clippy/Cargo.toml`

Caused by:
  No such file or directory (os error 2)
failed to run: /tmp/rust/build/x86_64-unknown-linux-gnu/stage0/bin/cargo build --manifest-path /tmp/rust/src/bootstrap/Cargo.toml

Full output: xpy-clippy.txt

/tmp/rust/src/tools/clippy/Cargo.toml should be in the clippy submodule but it's not checked out correctly. If I do git reset --hard inside the submodule, it works fine.

related #63964

@rustbot modify labels +A-rustbuild

[rustbot]

Error: Parsing label command in comment failed: ...'ify labels' | error: must have : or to as label starter at >| ' +A-rustbu'...

Please let @rust-lang/release know if you're having trouble with this bot.

[jethrogb]

@rustbot modify labels: +A-rustbuild

[jyn514]

This will become relevant again once #82208 is merged.