With git index verson = 4 and build script cargo can not build any project

[Dushistov]

Problem

Recently I tried https://www.git-tower.com/blog/git-performance/ to improve git performance,
but git update-index --index-version 4 breaks cargo.

Steps

❯ cargo new --bin demo2
     Created binary (application) `demo2` package
❯ cd demo2
❯ git update-index --show-index-version
0
❯ git add -A

❯ git commit -m "initial commit" -a
[master (root-commit) b49adb2] initial commit
 3 files changed, 12 insertions(+)
 create mode 100644 .gitignore
 create mode 100644 Cargo.toml
 create mode 100644 src/main.rs

❯ git config feature.manyFiles true
❯ git update-index --index-version 4
❯ git update-index --show-index-version
4
❯ git branch
* master

❯ PAGER= git log
commit b49adb2b54620710ee48e64bda608daf6029d47a (HEAD -> master)
Date:   Mon Dec 11 13:55:11 2023 +0300

    initial commit
❯ cargo build
   Compiling demo2 v0.1.0 (/tmp/demo2)
    Finished dev [unoptimized + debuginfo] target(s) in 0.13s

❯ echo "fn main() {}" > build.rs
❯ cargo check
error: failed to determine package fingerprint for build script for demo2 v0.1.0 (/tmp/demo2)

Caused by:
  failed to determine the most recently modified file in /tmp/demo2

Caused by:
  failed to determine list of files in /tmp/demo2

Caused by:
  failed to open git index at /tmp/demo2/.git/

Caused by:
  invalid data in index - calculated checksum does not match expected; class=Index (10)

Here is script to reproduce problem:

#!/bin/sh
#
set -euo pipefail

export LC_ALL=C
cd /tmp
cargo new --bin demo3
cd demo3
git update-index --show-index-version
git add -A
git commit -m "initial commit" -a
git config feature.manyFiles true
git update-index --index-version 4
git update-index --show-index-version
git branch
PAGER= git log
cargo build
echo "fn main() {}" > build.rs
cargo check

Possible Solution(s)

No response

Notes

No response

Version

❯ cargo version --verbose
cargo 1.75.0-beta.5 (1d8b05cdd 2023-11-20)
release: 1.75.0-beta.5
commit-hash: 1d8b05cdd1287c64467306cf3ca2c8ac60c11eb0
commit-date: 2023-11-20
host: x86_64-unknown-linux-gnu
libgit2: 1.7.1 (sys:0.18.1 vendored)
libcurl: 8.4.0-DEV (sys:0.4.68+curl-8.4.0 vendored ssl:OpenSSL/1.1.1u)
ssl: OpenSSL 1.1.1u  30 May 2023
os: Arch Linux Rolling Release [64-bit]

[ehuss]

Thanks for the report, and the detailed repro! This isn't exactly related to the index version, but is the consequence of feature.manyFiles enabling index.skipHash. This is tracked in #11857, so closing as a duplicate of that.