Skip untracked files in destroyed symlink checks

[j178]

Skip untracked-file enumeration in the destroyed-symlinks status query. Only tracked entries can identify a symlink replaced by a staged regular file.

[Copilot]

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[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-29T06:11:16.692559Z	bd36be1	PR opened

ℹ️ About Codex in GitHub

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• Mark a draft as ready
• Comment "@codex review" or "@codex security review".

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.26%. Comparing base (c80c853) to head (bd36be1).
⚠️ Report is 4 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2799      +/-   ##
==========================================
- Coverage   94.26%   94.26%   -0.01%     
==========================================
  Files         142      142              
  Lines       30743    30749       +6     
==========================================
+ Hits        28980    28985       +5     
- Misses       1763     1764       +1     

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[prek-ci-bot]

📦 Cargo Bloat Comparison

.text size change: +0.00% (12.8 MiB → 12.8 MiB)

Expand for cargo-bloat output

Head Branch Results

File  .text     Size             Crate Name
0.1%   2.5% 332.0KiB        aws_lc_sys aws_lc_0_45_0_aes_gcm_encrypt_avx512
0.1%   2.5% 332.0KiB        aws_lc_sys aws_lc_0_45_0_aes_gcm_decrypt_avx512
0.0%   0.7%  88.6KiB              prek <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
0.0%   0.4%  49.8KiB              prek <<prek::config::hook::HookWire as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<&mut <serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
0.0%   0.4%  48.7KiB annotate_snippets annotate_snippets::renderer::render::render
0.0%   0.4%  46.7KiB              prek <<prek::config::Config as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<&mut <serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
0.0%   0.3%  38.5KiB              prek prek::cli::run::run::run::{closure#0}
0.0%   0.3%  37.4KiB              prek prek::run::{closure#0}
0.0%   0.2%  31.8KiB              prek <prek::languages::rust::rust::Rust as prek::languages::LanguageBackend>::install::{closure#0}
0.0%   0.2%  29.8KiB              prek <prek::cli::RunOptions as clap_builder::derive::Args>::augment_args
0.0%   0.2%  29.1KiB      serde_saphyr <granit_parser::scanner::Scanner<granit_parser::input::str::StrInput>>::fetch_more_tokens
0.0%   0.2%  28.6KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  28.1KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  28.0KiB              toml <toml::de::deserializer::value::ValueDeserializer as serde_core::de::Deserializer>::deserialize_any::<<prek::config::hook::HookWire as serde_core::de::Deserialize>::deserialize::__Visitor>
0.0%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_45_0_edwards25519_scalarmuldouble_alt
0.0%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_45_0_edwards25519_scalarmuldouble
0.0%   0.2%  27.3KiB              prek <prek::languages::ruby::installer::RubyInstaller>::install::{closure#0}
0.0%   0.2%  27.1KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  27.1KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  27.1KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
4.1%  87.1%  11.2MiB                   And 20722 smaller methods. Use -n N to show more.
4.7% 100.0%  12.8MiB                   .text section size, the file size is 273.8MiB

Base Branch Results

File  .text     Size             Crate Name
0.1%   2.5% 332.0KiB        aws_lc_sys aws_lc_0_45_0_aes_gcm_encrypt_avx512
0.1%   2.5% 332.0KiB        aws_lc_sys aws_lc_0_45_0_aes_gcm_decrypt_avx512
0.0%   0.7%  88.6KiB              prek <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
0.0%   0.4%  49.8KiB              prek <<prek::config::hook::HookWire as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<&mut <serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
0.0%   0.4%  48.7KiB annotate_snippets annotate_snippets::renderer::render::render
0.0%   0.4%  46.7KiB              prek <<prek::config::Config as serde_core::de::Deserialize>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map::<&mut <serde_saphyr::de::deserializer::YamlDeserializer as serde_core::de::Deserializer>::deserialize_map::MA>
0.0%   0.3%  38.5KiB              prek prek::cli::run::run::run::{closure#0}
0.0%   0.3%  37.4KiB              prek prek::run::{closure#0}
0.0%   0.2%  31.8KiB              prek <prek::languages::rust::rust::Rust as prek::languages::LanguageBackend>::install::{closure#0}
0.0%   0.2%  29.8KiB              prek <prek::cli::RunOptions as clap_builder::derive::Args>::augment_args
0.0%   0.2%  29.1KiB      serde_saphyr <granit_parser::scanner::Scanner<granit_parser::input::str::StrInput>>::fetch_more_tokens
0.0%   0.2%  28.6KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  28.1KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  28.0KiB              toml <toml::de::deserializer::value::ValueDeserializer as serde_core::de::Deserializer>::deserialize_any::<<prek::config::hook::HookWire as serde_core::de::Deserialize>::deserialize::__Visitor>
0.0%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_45_0_edwards25519_scalarmuldouble_alt
0.0%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_45_0_edwards25519_scalarmuldouble
0.0%   0.2%  27.3KiB              prek <prek::languages::ruby::installer::RubyInstaller>::install::{closure#0}
0.0%   0.2%  27.1KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  27.1KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
0.0%   0.2%  27.1KiB              prek prek::archive::unpack::<fs_err::tokio::file::File, &std::path::PathBuf>::{closure#0}
4.1%  87.1%  11.2MiB                   And 20722 smaller methods. Use -n N to show more.
4.7% 100.0%  12.8MiB                   .text section size, the file size is 273.8MiB

[prek-ci-bot]

⚡️ Hyperfine Benchmarks

Summary: 4 regressions, 8 improvements above the 10% threshold.

Environment

• OS: Linux 6.17.0-1022-azure
• CPU: 4 cores
• prek version: prek 0.5.4+8 (1eb2ffe 2026-09-29)
• Rust version: rustc 1.98.1 (48a229cea 2026-09-01)
• 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	1.5 ± 0.1	1.3	1.8	1.00
prek-head --version	1.5 ± 0.1	1.4	1.7	1.04 ± 0.10

prek list

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base list	9.1 ± 7.1	6.4	63.6	1.06 ± 1.06
prek-head list	8.5 ± 5.3	6.9	45.6	1.00

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	5.3 ± 11.9	2.2	70.8	1.00
prek-head sample-config	6.6 ± 14.4	2.2	86.2	1.24 ± 3.85

⚠️ Warning: Performance regression for prek sample-config: 23.6700% slower

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	12.0 ± 0.7	11.6	13.7	1.00
prek-head run --all-files	12.1 ± 0.4	11.6	12.7	1.00 ± 0.07

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --all-files	12.9 ± 0.5	11.9	13.8	1.06 ± 0.07
prek-head run --all-files	12.2 ± 0.7	11.4	13.3	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	11.9 ± 0.6	11.1	13.6	1.00
prek-head run --all-files	12.8 ± 5.3	11.0	48.2	1.08 ± 0.45

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	5.9 ± 1.3	5.4	12.6	1.01 ± 0.23
prek-head run trailing-whitespace --all-files	5.9 ± 0.4	5.3	6.8	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	13.7 ± 27.6	4.9	135.3	1.66 ± 4.29
prek-head run end-of-file-fixer --all-files	8.2 ± 13.2	5.0	77.4	1.00

✅ Performance improvement for prek run end-of-file-fixer --all-files: 39.8300% faster

prek run check-json --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-json --all-files	8.3 ± 8.8	4.5	45.5	1.00
prek-head run check-json --all-files	14.5 ± 20.8	4.7	89.8	1.75 ± 3.12

⚠️ Warning: Performance regression for prek run check-json --all-files: 74.8100% slower

prek run check-yaml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-yaml --all-files	6.8 ± 4.9	4.7	25.8	1.00
prek-head run check-yaml --all-files	6.8 ± 7.8	4.6	47.1	1.01 ± 1.37

prek run check-toml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-toml --all-files	5.4 ± 2.9	4.6	20.6	1.09 ± 0.63
prek-head run check-toml --all-files	4.9 ± 0.9	4.5	9.3	1.00

prek run check-xml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-xml --all-files	8.7 ± 15.4	4.5	84.7	1.36 ± 2.87
prek-head run check-xml --all-files	6.4 ± 7.3	4.6	43.9	1.00

✅ Performance improvement for prek run check-xml --all-files: 26.7200% faster

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run detect-private-key --all-files	10.9 ± 20.3	4.8	106.4	1.61 ± 3.43
prek-head run detect-private-key --all-files	6.7 ± 6.9	4.8	41.2	1.00

✅ Performance improvement for prek run detect-private-key --all-files: 38.0100% faster

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	13.9 ± 19.9	4.8	90.6	2.28 ± 3.50
prek-head run fix-byte-order-marker --all-files	6.1 ± 3.3	4.8	21.3	1.00

✅ Performance improvement for prek run fix-byte-order-marker --all-files: 56.2200% faster

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	32.1 ± 39.3	3.4	78.3	9.10 ± 11.13
prek-head install-hooks	3.5 ± 0.1	3.5	3.6	1.00

✅ Performance improvement for prek install-hooks (cold - no cache): 89.0200% faster

prek install-hooks (warm - with cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base install-hooks	7.1 ± 8.1	3.4	21.6	1.00
prek-head install-hooks	7.7 ± 9.6	3.3	24.9	1.08 ± 1.84

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	16.1 ± 7.5	11.9	37.5	1.00
prek-head run	26.3 ± 27.5	11.9	105.0	1.63 ± 1.87

⚠️ Warning: Performance regression for prek run (staged files only): 63.1800% slower

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --files '*.json'	8.3 ± 19.2	3.7	90.0	1.43 ± 3.75
prek-head run --files '*.json'	5.8 ± 7.1	3.7	35.9	1.00

✅ Performance improvement for prek run --files '*.json' (specific file type): 29.8600% faster

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	15.0 ± 25.9	4.6	113.1	2.47 ± 4.83
prek-head run --dry-run --all-files	6.1 ± 5.5	4.7	29.3	1.00

✅ Performance improvement for prek run --dry-run --all-files (measures init overhead): 59.5900% faster

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	5.7 ± 0.2	5.5	6.2	1.00
prek-head run check-hooks-apply --all-files	14.8 ± 31.8	5.4	129.6	2.59 ± 5.59

⚠️ Warning: Performance regression for prek run check-hooks-apply --all-files: 159.4100% slower

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-useless-excludes --all-files	11.2 ± 22.1	5.4	91.2	2.01 ± 3.95
prek-head run check-useless-excludes --all-files	5.6 ± 0.2	5.4	6.3	1.00

✅ Performance improvement for prek run check-useless-excludes --all-files: 50.2500% faster

prek run identity --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run identity --all-files	11.6 ± 22.3	4.6	90.8	1.00
prek-head run identity --all-files	11.8 ± 25.2	4.7	102.4	1.01 ± 2.90