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Expose the git work tree to hooks running outside the git root - #2579

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j178 merged 4 commits into
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jeromeheissler:fix-hook-work-tree-linked-worktree
Aug 19, 2026
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Expose the git work tree to hooks running outside the git root#2579
j178 merged 4 commits into
j178:masterfrom
jeromeheissler:fix-hook-work-tree-linked-worktree

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@jeromeheissler jeromeheissler commented Aug 18, 2026

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Committing from a linked worktree (git worktree add) makes Git export an
absolute GIT_DIR to hooks without a GIT_WORK_TREE. Git then treats the
current directory as the work tree root. Committing from a main worktree
exports neither, so only linked worktrees are affected.

prek runs each workspace project's hooks with the cwd set to that project's
directory. In a linked worktree that made a hook's own Git command resolve the
repository root to the sub-project directory: git add -u inside a
sub-project hook rewrote the whole index as if the sub-project were the
repository, staging every path outside it as deleted and giving the surviving
paths the sub-project's blobs.

prek already derives the correct work tree in init_git_work_tree, but #2356
scoped it to prek's own Git commands so hooks do not inherit an environment Git
did not expose. Keep that scoping, with one exception: hook subprocesses that
start outside the git root, which is exactly the sub-project case. Hooks
running at the git root are unaffected, so #2293 stays fixed.

Related: #2505 isolated the same environment leak for dependency installs, but
hook execution still inherits it.

@jeromeheissler
Expose the git work tree to hooks running outside the git root
5e1271d 
Committing from a linked worktree makes Git export an absolute `GIT_DIR`
without a `GIT_WORK_TREE`, which tells Git to treat the current directory
as the work tree root. Workspace hooks run in their own project
directory, so a Git command inside such a hook resolved the repository
root to that subdirectory and rewrote the index as if the sub-project
were the whole repository.

Pass the derived work tree to hook subprocesses that start outside the
git root. Hooks that run at the git root already resolve the root
correctly, so they keep inheriting the environment Git gave us.
@jeromeheissler
jeromeheissler requested a review from j178 as a code owner August 18, 2026 08:25
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.78%. Comparing base (7821d28) to head (7c3cc5a).
⚠️ Report is 3 commits behind head on master.

Additional details and impacted files 
@@           Coverage Diff           @@
##           master    #2579   +/-   ##
=======================================
  Coverage   93.78%   93.78%           
=======================================
  Files         140      140           
  Lines       29036    29058   +22     
=======================================
+ Hits        27230    27251   +21     
- Misses       1806     1807    +1

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Comment thread crates/prek/src/languages/mod.rs Outdated
@jeromeheissler
Route Julia hooks through the hook work tree helper
ae0144d 
`Julia::run` builds its own command instead of going through
`ExecutionEnvironment::command`, so Julia hooks in a workspace kept
inheriting `GIT_DIR` without the derived `GIT_WORK_TREE` and could still
rewrite the index from a linked worktree.

Move the environment handling into `git::apply_hook_work_tree` and call
it from both runners. The other backends that build their own commands
are unaffected: `docker` and `docker_image` only forward the variables
they pass with `-e`, `pygrep` runs a script prek ships itself, and
`fail` starts no process at all.
@prek-ci-bot

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📦 Cargo Bloat Comparison

Binary size change: +0.00% (30.3 MiB → 30.3 MiB)

Expand for cargo-bloat output

Head Branch Results

 File  .text     Size             Crate Name
 1.1%   2.2% 332.0KiB        aws_lc_sys aws_lc_0_44_0_aes_gcm_encrypt_avx512
 1.1%   2.2% 332.0KiB        aws_lc_sys aws_lc_0_44_0_aes_gcm_decrypt_avx512
 0.2%   0.5%  74.9KiB              prek <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.2%   0.4%  57.9KiB              prek prek::run::{closure#0}
 0.2%   0.4%  54.1KiB              prek <<prek::config::hook::HookWire as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<<serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
 0.2%   0.3%  49.4KiB annotate_snippets annotate_snippets::renderer::render::render
 0.2%   0.3%  48.3KiB              prek <<prek::config::Config as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<<serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
 0.1%   0.3%  45.0KiB              prek prek::cli::run::run::run::{closure#0}
 0.1%   0.2%  33.9KiB              prek <prek::cli::RunOptions as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  32.7KiB              prek <prek::languages::ruby::installer::RubyInstaller>::install::{closure#0}
 0.1%   0.2%  29.4KiB     granit_parser <granit_parser::scanner::Scanner<granit_parser::input::str::StrInput>>::fetch_more_tokens
 0.1%   0.2%  28.8KiB     granit_parser <granit_parser::scanner::Scanner<granit_parser::input::str::StrInput>>::fetch_more_tokens
 0.1%   0.2%  28.6KiB    cargo_metadata <&mut serde_json::de::Deserializer<serde_json::read::StrRead> as serde_core::de::Deserializer>::deserialize_struct::<<cargo_metadata::Package as serde_core::de::Deserialize>::deserialize::__Visitor>
 0.1%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_44_0_edwards25519_scalarmuldouble_alt
 0.1%   0.2%  27.7KiB              prek <prek::languages::mise::installer::MiseInstaller>::download::{closure#0}
 0.1%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_44_0_edwards25519_scalarmuldouble
 0.1%   0.2%  25.9KiB              prek prek::cli::try_repo::try_repo::{closure#0}
 0.1%   0.2%  24.6KiB              prek <prek::languages::node::installer::NodeInstaller>::install::{closure#0}
 0.1%   0.2%  23.7KiB              prek <<prek::config::update::UpdateOptions as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<<serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
 0.1%   0.2%  23.2KiB               xml <xml::reader::parser::PullParser>::dispatch_token
42.8%  88.4%  12.9MiB                   And 26749 smaller methods. Use -n N to show more.
48.4% 100.0%  14.6MiB                   .text section size, the file size is 30.3MiB

Base Branch Results

 File  .text     Size             Crate Name
 1.1%   2.2% 332.0KiB        aws_lc_sys aws_lc_0_44_0_aes_gcm_encrypt_avx512
 1.1%   2.2% 332.0KiB        aws_lc_sys aws_lc_0_44_0_aes_gcm_decrypt_avx512
 0.3%   0.6%  87.9KiB              prek <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.2%   0.4%  57.3KiB              prek prek::run::{closure#0}
 0.2%   0.4%  53.5KiB              prek <<prek::config::hook::HookWire as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<<serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
 0.2%   0.3%  49.4KiB annotate_snippets annotate_snippets::renderer::render::render
 0.2%   0.3%  48.3KiB              prek <<prek::config::Config as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<<serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
 0.1%   0.3%  46.2KiB              prek <prek::languages::ruby::installer::RubyInstaller>::install::{closure#0}
 0.1%   0.3%  40.3KiB              prek prek::cli::run::run::run::{closure#0}
 0.1%   0.3%  37.7KiB              prek <prek::languages::node::installer::NodeInstaller>::install::{closure#0}
 0.1%   0.2%  34.1KiB              prek <prek::cli::RunOptions as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  33.2KiB              prek <prek::languages::golang::installer::GoInstaller>::install::{closure#0}
 0.1%   0.2%  31.3KiB              prek <prek::languages::bun::installer::BunInstaller>::install::{closure#0}
 0.1%   0.2%  29.4KiB     granit_parser <granit_parser::scanner::Scanner<granit_parser::input::str::StrInput>>::fetch_more_tokens
 0.1%   0.2%  29.1KiB              prek <prek::languages::deno::installer::DenoInstaller>::download::{closure#0}
 0.1%   0.2%  28.8KiB     granit_parser <granit_parser::scanner::Scanner<granit_parser::input::str::StrInput>>::fetch_more_tokens
 0.1%   0.2%  28.6KiB    cargo_metadata <&mut serde_json::de::Deserializer<serde_json::read::StrRead> as serde_core::de::Deserializer>::deserialize_struct::<<cargo_metadata::Package as serde_core::de::Deserialize>::deserialize::__Visitor>
 0.1%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_44_0_edwards25519_scalarmuldouble_alt
 0.1%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_44_0_edwards25519_scalarmuldouble
 0.1%   0.2%  27.0KiB              prek <prek::languages::mise::installer::MiseInstaller>::download::{closure#0}
42.6%  88.0%  12.9MiB                   And 26770 smaller methods. Use -n N to show more.
48.4% 100.0%  14.7MiB                   .text section size, the file size is 30.3MiB

@prek-ci-bot

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⚡️ Hyperfine Benchmarks

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

Environment
  • OS: Linux 6.17.0-1022-azure
  • CPU: 4 cores
  • prek version: prek 0.4.14+12 (e75a7f5 2026-08-19)
  • Rust version: rustc 1.97.1 (8bab26f4f 2026-07-14)
  • 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 2.2 ± 0.1 2.1 2.6 1.02 ± 0.15
prek-head --version 2.2 ± 0.3 2.1 5.0 1.00

prek list

Command Mean [ms] Min [ms] Max [ms] Relative
prek-base list 9.3 ± 0.3 9.0 11.6 1.00
prek-head list 9.3 ± 0.2 9.0 10.0 1.00 ± 0.04

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

⏭️ Skipped: .pre-commit-config.yaml not found

prek sample-config

Command Mean [ms] Min [ms] Max [ms] Relative
prek-base sample-config 2.6 ± 0.3 2.4 4.9 1.01 ± 0.14
prek-head sample-config 2.5 ± 0.0 2.5 2.7 1.00
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 40.2 ± 0.9 38.7 41.2 1.00
prek-head run --all-files 40.4 ± 1.3 37.7 42.2 1.01 ± 0.04

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

Command Mean [ms] Min [ms] Max [ms] Relative
prek-base run --all-files 41.0 ± 1.2 38.8 42.8 1.02 ± 0.04
prek-head run --all-files 40.1 ± 1.0 37.8 41.8 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 40.1 ± 1.6 36.7 44.4 1.00 ± 0.05
prek-head run --all-files 39.9 ± 1.0 37.7 42.5 1.00
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 13.5 ± 0.4 12.7 14.4 1.00
prek-head run trailing-whitespace --all-files 13.7 ± 0.6 12.8 15.4 1.02 ± 0.05

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 11.5 ± 0.5 10.5 13.3 1.00
prek-head run end-of-file-fixer --all-files 11.7 ± 0.5 10.8 12.7 1.02 ± 0.07

prek run check-json --all-files

Command Mean [ms] Min [ms] Max [ms] Relative
prek-base run check-json --all-files 8.0 ± 0.3 7.6 8.5 1.00
prek-head run check-json --all-files 8.7 ± 1.2 7.5 13.6 1.08 ± 0.15

prek run check-yaml --all-files

Command Mean [ms] Min [ms] Max [ms] Relative
prek-base run check-yaml --all-files 8.2 ± 0.2 7.8 8.7 1.00
prek-head run check-yaml --all-files 8.6 ± 0.2 8.1 8.9 1.05 ± 0.04

prek run check-toml --all-files

Command Mean [ms] Min [ms] Max [ms] Relative
prek-base run check-toml --all-files 8.5 ± 0.3 8.0 9.4 1.00
prek-head run check-toml --all-files 8.5 ± 0.4 8.0 9.7 1.00 ± 0.06

prek run check-xml --all-files

Command Mean [ms] Min [ms] Max [ms] Relative
prek-base run check-xml --all-files 8.3 ± 0.4 7.9 9.6 1.02 ± 0.08
prek-head run check-xml --all-files 8.1 ± 0.6 7.4 9.7 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 11.8 ± 0.6 10.8 13.7 1.02 ± 0.07
prek-head run detect-private-key --all-files 11.6 ± 0.6 10.7 12.6 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 13.5 ± 0.9 12.5 15.3 1.00
prek-head run fix-byte-order-marker --all-files 13.9 ± 1.0 12.4 15.9 1.03 ± 0.10
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 4.6 ± 0.1 4.5 4.7 1.01 ± 0.03
prek-head install-hooks 4.5 ± 0.1 4.4 4.6 1.00

prek install-hooks (warm - with cache)

Command Mean [ms] Min [ms] Max [ms] Relative
prek-base install-hooks 4.5 ± 0.0 4.5 4.5 1.00
prek-head install-hooks 4.6 ± 0.1 4.4 4.7 1.00 ± 0.02
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 24.1 ± 0.5 23.3 25.1 1.00
prek-head run 24.7 ± 0.5 23.8 25.7 1.03 ± 0.03

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

Command Mean [ms] Min [ms] Max [ms] Relative
prek-base run --files '*.json' 5.4 ± 0.2 5.2 5.9 1.00
prek-head run --files '*.json' 5.5 ± 0.1 5.3 5.6 1.02 ± 0.03
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 7.0 ± 0.2 6.8 7.4 1.02 ± 0.03
prek-head run --dry-run --all-files 6.8 ± 0.1 6.7 7.0 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 8.2 ± 0.2 7.9 8.5 1.00
prek-head run check-hooks-apply --all-files 8.3 ± 0.2 8.1 8.6 1.02 ± 0.03

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

Command Mean [ms] Min [ms] Max [ms] Relative
prek-base run check-useless-excludes --all-files 8.3 ± 0.1 8.0 8.6 1.00 ± 0.02
prek-head run check-useless-excludes --all-files 8.2 ± 0.1 8.0 8.5 1.00

prek run identity --all-files

Command Mean [ms] Min [ms] Max [ms] Relative
prek-base run identity --all-files 7.2 ± 0.1 7.0 7.4 1.00 ± 0.02
prek-head run identity --all-files 7.1 ± 0.1 7.0 7.2 1.00

@j178 j178 mentioned this pull request Aug 19, 2026
Merged
@j178
j178 force-pushed the fix-hook-work-tree-linked-worktree branch from 80c4e5a to 7c3cc5a Compare August 19, 2026 05:19
@j178 j178 added the bug Something isn't working label Aug 19, 2026
@j178
j178 merged commit 01da036 into j178:master Aug 19, 2026
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j178 added a commit that referenced this pull request Aug 19, 2026
@j178
Document Git environment handling in hooks (#2582)
7bcacc8 
Documents the Git environment contract for hooks and how to isolate Git
commands that operate on a separate repository.

Stacked on #2579.
@j178

j178 commented Aug 19, 2026

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