Remove GIT_INDEX_FILE from env before running hooks

[souliane]

Summary

Fixes #1786

When git commit -a invokes the pre-commit hook, GIT_INDEX_FILE points to .git/index.lock. If a hook subprocess (e.g., a test suite like pytest) runs git commands internally, those commands read/write the lock file instead of the normal .git/index, corrupting the lock. Prek's subsequent git diff then fails with fatal: unable to read <hash>.

This PR strips GIT_INDEX_FILE from the process environment after prek's own git operations (write-tree, diff-index, collect-files) but before hook execution.

Reproduction

git clone https://github.com/souliane/prek-issue-1786-repro.git
cd prek-issue-1786-repro
prek install
git commit -a -m "test"
# → fatal: unable to read <hash>

The repro repo has a single hook that runs git init + git add in a temp directory (simulating what happens when a test suite runs tests that invoke git commands). The inherited GIT_INDEX_FILE causes the temp dir's git add to write to the parent repo's .git/index.lock.

Verification

After this fix, git commit -a -m "test" on the repro repo succeeds.

Note: I don't have a Rust toolchain installed locally, so I couldn't run the test suite. CI should validate the build. If you'd like me to add a test case, let me know the preferred pattern.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.72%. Comparing base (9782923) to head (089f9d2).
⚠️ Report is 3 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1815   +/-   ##
=======================================
  Coverage   91.72%   91.72%           
=======================================
  Files          98       98           
  Lines       20055    20055           
=======================================
  Hits        18395    18395           
  Misses       1660     1660           

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[prek-ci-bot]

📦 Cargo Bloat Comparison

Binary size change: +0.00% (24.8 MiB → 24.8 MiB)

Expand for cargo-bloat output

Head Branch Results

 File  .text     Size             Crate Name
 1.3%   2.7% 332.0KiB        aws_lc_sys aws_lc_0_38_0_aes_gcm_encrypt_avx512
 1.3%   2.7% 332.0KiB        aws_lc_sys aws_lc_0_38_0_aes_gcm_decrypt_avx512
 0.3%   0.7%  81.7KiB             prek? <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.3%   0.6%  77.6KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.6%  69.8KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.2%   0.4%  51.0KiB annotate_snippets annotate_snippets::renderer::render::render
 0.2%   0.4%  50.6KiB              prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.2%   0.4%  46.1KiB              prek prek::run::{{closure}}
 0.2%   0.3%  41.8KiB              prek prek::cli::run::run::run::{{closure}}
 0.1%   0.3%  32.0KiB             prek? <prek::cli::RunArgs as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_38_0_edwards25519_scalarmuldouble_alt
 0.1%   0.2%  27.8KiB      serde_saphyr saphyr_parser_bw::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_38_0_edwards25519_scalarmuldouble
 0.1%   0.2%  25.8KiB              prek prek::cli::try_repo::try_repo::{{closure}}
 0.1%   0.2%  25.3KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::Config>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.1%   0.2%  23.2KiB              prek prek::hooks::meta_hooks::MetaHooks::run::{{closure}}
 0.1%   0.2%  22.4KiB      serde_saphyr saphyr_parser_bw::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  22.3KiB         [Unknown] Lp384_montjscalarmul_alt_p384_montjadd
 0.1%   0.2%  22.0KiB               std core::ptr::drop_in_place<prek::languages::<impl prek::config::Language>::install::{{closure}}>
 0.1%   0.2%  21.6KiB              prek prek::workspace::Project::init_hooks::{{closure}}
41.1%  85.9%  10.2MiB                   And 23310 smaller methods. Use -n N to show more.
47.8% 100.0%  11.9MiB                   .text section size, the file size is 24.8MiB

Base Branch Results

 File  .text     Size             Crate Name
 1.3%   2.7% 332.0KiB        aws_lc_sys aws_lc_0_38_0_aes_gcm_encrypt_avx512
 1.3%   2.7% 332.0KiB        aws_lc_sys aws_lc_0_38_0_aes_gcm_decrypt_avx512
 0.3%   0.7%  81.7KiB             prek? <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.3%   0.6%  77.6KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.6%  69.8KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.2%   0.4%  51.0KiB annotate_snippets annotate_snippets::renderer::render::render
 0.2%   0.4%  50.6KiB              prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.2%   0.4%  46.1KiB              prek prek::run::{{closure}}
 0.2%   0.3%  41.8KiB              prek prek::cli::run::run::run::{{closure}}
 0.1%   0.3%  32.0KiB             prek? <prek::cli::RunArgs as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_38_0_edwards25519_scalarmuldouble_alt
 0.1%   0.2%  27.8KiB      serde_saphyr saphyr_parser_bw::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_38_0_edwards25519_scalarmuldouble
 0.1%   0.2%  25.8KiB              prek prek::cli::try_repo::try_repo::{{closure}}
 0.1%   0.2%  25.3KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::Config>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.1%   0.2%  23.2KiB              prek prek::hooks::meta_hooks::MetaHooks::run::{{closure}}
 0.1%   0.2%  22.4KiB      serde_saphyr saphyr_parser_bw::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  22.3KiB         [Unknown] Lp384_montjscalarmul_alt_p384_montjadd
 0.1%   0.2%  22.0KiB               std core::ptr::drop_in_place<prek::languages::<impl prek::config::Language>::install::{{closure}}>
 0.1%   0.2%  21.6KiB              prek prek::workspace::Project::init_hooks::{{closure}}
41.1%  85.9%  10.2MiB                   And 23317 smaller methods. Use -n N to show more.
47.8% 100.0%  11.9MiB                   .text section size, the file size is 24.8MiB

[prek-ci-bot]

⚡️ Hyperfine Benchmarks

Summary: 0 regressions, 0 improvements above the 10% threshold.

Environment

• OS: Linux 6.14.0-1017-azure
• CPU: 4 cores
• prek version: prek 0.3.6+8 (fbdfd05 2026-03-17)
• Rust version: rustc 1.94.0 (4a4ef493e 2026-03-02)
• Hyperfine version: hyperfine 1.20.0

CLI Commands

Benchmarking basic commands in the main repo:

prek --version

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base --version	2.5 ± 0.2	2.3	3.6	1.01 ± 0.08
prek-head --version	2.4 ± 0.1	2.3	2.6	1.00

prek list

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base list	9.5 ± 0.2	9.1	10.3	1.00 ± 0.03
prek-head list	9.4 ± 0.2	9.1	9.8	1.00

prek validate-config .pre-commit-config.yaml

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base validate-config .pre-commit-config.yaml	3.2 ± 0.1	3.1	3.4	1.00
prek-head validate-config .pre-commit-config.yaml	3.3 ± 0.1	3.2	3.6	1.02 ± 0.03

prek sample-config

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base sample-config	2.8 ± 0.1	2.6	2.9	1.00
prek-head sample-config	2.8 ± 0.1	2.6	2.9	1.00 ± 0.03

Cold vs Warm Runs

Comparing first run (cold) vs subsequent runs (warm cache):

prek run --all-files (cold - no cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --all-files	159.6 ± 1.6	156.3	161.4	1.00
prek-head run --all-files	161.2 ± 2.2	158.6	165.5	1.01 ± 0.02

prek run --all-files (warm - with cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --all-files	164.7 ± 3.3	160.0	171.2	1.02 ± 0.03
prek-head run --all-files	161.6 ± 3.5	156.8	170.3	1.00

Full Hook Suite

Running the builtin hook suite on the benchmark workspace:

prek run --all-files (full builtin hook suite)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --all-files	162.9 ± 3.7	156.9	173.5	1.00
prek-head run --all-files	165.7 ± 25.2	156.4	338.2	1.02 ± 0.16

Individual Hook Performance

Benchmarking each hook individually on the test repo:

prek run trailing-whitespace --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run trailing-whitespace --all-files	23.1 ± 0.5	22.1	24.2	1.03 ± 0.03
prek-head run trailing-whitespace --all-files	22.5 ± 0.3	21.8	23.0	1.00

prek run end-of-file-fixer --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run end-of-file-fixer --all-files	30.5 ± 2.3	26.4	35.3	1.04 ± 0.10
prek-head run end-of-file-fixer --all-files	29.4 ± 1.7	27.0	33.8	1.00

prek run check-json --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-json --all-files	13.5 ± 0.4	12.3	14.2	1.05 ± 0.05
prek-head run check-json --all-files	12.8 ± 0.4	12.1	13.5	1.00

prek run check-yaml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-yaml --all-files	12.5 ± 0.3	12.0	13.3	1.03 ± 0.03
prek-head run check-yaml --all-files	12.2 ± 0.3	11.7	12.9	1.00

prek run check-toml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-toml --all-files	12.3 ± 0.3	11.9	13.0	1.00 ± 0.03
prek-head run check-toml --all-files	12.2 ± 0.3	11.7	12.7	1.00

prek run check-xml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-xml --all-files	12.5 ± 0.3	12.1	13.7	1.03 ± 0.03
prek-head run check-xml --all-files	12.2 ± 0.2	11.8	12.6	1.00

prek run detect-private-key --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run detect-private-key --all-files	19.6 ± 1.6	17.4	23.0	1.03 ± 0.12
prek-head run detect-private-key --all-files	19.0 ± 1.5	16.8	22.0	1.00

prek run fix-byte-order-marker --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run fix-byte-order-marker --all-files	25.1 ± 1.5	21.6	29.2	1.00
prek-head run fix-byte-order-marker --all-files	25.5 ± 1.7	22.0	29.2	1.02 ± 0.09

Installation Performance

Benchmarking hook installation (fast path hooks skip Python setup):

prek install-hooks (cold - no cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base install-hooks	5.0 ± 0.1	4.9	5.1	1.01 ± 0.03
prek-head install-hooks	4.9 ± 0.1	4.8	5.1	1.00

prek install-hooks (warm - with cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base install-hooks	5.1 ± 0.1	5.0	5.2	1.01 ± 0.02
prek-head install-hooks	5.0 ± 0.1	5.0	5.1	1.00

File Filtering/Scoping Performance

Testing different file selection modes:

prek run (staged files only)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run	54.5 ± 1.3	52.1	57.0	1.00 ± 0.04
prek-head run	54.4 ± 1.4	52.8	58.1	1.00

prek run --files '*.json' (specific file type)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --files '*.json'	9.5 ± 0.2	9.3	9.7	1.00 ± 0.03
prek-head run --files '*.json'	9.5 ± 0.2	9.2	10.1	1.00

Workspace Discovery & Initialization

Benchmarking hook discovery and initialization overhead:

prek run --dry-run --all-files (measures init overhead)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --dry-run --all-files	14.5 ± 0.7	14.0	17.4	1.01 ± 0.05
prek-head run --dry-run --all-files	14.4 ± 0.2	14.0	14.9	1.00

Meta Hooks Performance

Benchmarking meta hooks separately:

prek run check-hooks-apply --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-hooks-apply --all-files	13.0 ± 0.2	12.8	13.5	1.00
prek-head run check-hooks-apply --all-files	13.1 ± 0.2	12.8	13.4	1.00 ± 0.02

prek run check-useless-excludes --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-useless-excludes --all-files	12.9 ± 0.1	12.7	13.1	1.00
prek-head run check-useless-excludes --all-files	12.9 ± 0.1	12.7	13.0	1.00 ± 0.01

prek run identity --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run identity --all-files	11.4 ± 0.1	11.1	11.6	1.00
prek-head run identity --all-files	11.4 ± 0.1	11.2	11.6	1.00 ± 0.01