feat(install): warn about hooks that won't run with the installed shims

[BitWeaverDev]

Closes #2056

What

prek install only installs shims for the hook types you ask for — --hook-type, or default_install_hook_types, falling back to pre-commit. If the config has hooks pinned to a different stage (the classic case being a slower stages: [pre-push] hook), those hooks just silently never run after a plain prek install, and it's easy not to notice.

This adds a warning at install time that names the hooks whose stages aren't covered and points at the fix:

warning: The following hooks won't run automatically because their stages aren't being installed:
  - `push-only` (pre-push)
hint: install the missing hook type(s) with `prek install --hook-type <type>`, or set `default_install_hook_types` in your config.

Notes on the approach

• Config only, no hook init. Each hook's stages are resolved straight from config (stages → default_stages → all), so install stays offline and fast. The trade-off is that a remote hook narrowed only by its manifest (not by the project config) won't be flagged — that's the conservative choice: no false positives, no new network I/O, and it covers the case from the issue.
• manual is skipped, since manual-only hooks have no Git shim and aren't meant to run automatically.
• Pulled the hook-stage resolution into Stages::resolve so install and HookSpec::apply_project_defaults share one implementation instead of duplicating the fallback rules.
• No behaviour change to anything that runs — it's purely an extra warning.

Tests

Added integration coverage in tests/install.rs: an unmatched hook warns (while an all-stages sibling does not), installing the matching --hook-type silences it, manual-only never warns, and default_stages inheritance is taken into account.

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[codecov]

Codecov Report

❌ Patch coverage is 96.07843% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.57%. Comparing base (6166275) to head (e19b651).

Files with missing lines	Patch %	Lines
crates/prek/src/cli/install.rs	96.29%	3 Missing ⚠️
crates/prek/src/config.rs	94.73%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2205      +/-   ##
==========================================
- Coverage   92.59%   92.57%   -0.02%     
==========================================
  Files         125      125              
  Lines       26587    26680      +93     
==========================================
+ Hits        24617    24699      +82     
- Misses       1970     1981      +11     

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[prek-ci-bot]

📦 Cargo Bloat Comparison

Binary size change: +0.00% (26.6 MiB → 26.6 MiB)

Expand for cargo-bloat output

Head Branch Results

 File  .text     Size             Crate Name
 1.2%   2.5% 332.0KiB        aws_lc_sys aws_lc_0_41_0_aes_gcm_encrypt_avx512
 1.2%   2.5% 332.0KiB        aws_lc_sys aws_lc_0_41_0_aes_gcm_decrypt_avx512
 0.4%   0.7%  95.5KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.7%  91.3KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.6%  85.0KiB              prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.2%   0.5%  65.2KiB             prek? <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.2%   0.4%  49.4KiB annotate_snippets annotate_snippets::renderer::render::render
 0.2%   0.4%  49.0KiB              prek prek::run::{{closure}}
 0.2%   0.3%  44.6KiB              prek prek::cli::run::run::run::{{closure}}
 0.2%   0.3%  43.8KiB             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%  31.9KiB             prek? <prek::cli::RunOptions as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  31.8KiB               std core::ptr::drop_in_place<prek::languages::<impl prek::config::Language>::install::{{closure}}>
 0.1%   0.2%  29.4KiB     granit_parser granit_parser::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_41_0_edwards25519_scalarmuldouble_alt
 0.1%   0.2%  27.5KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::RemoteHook>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.1%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_41_0_edwards25519_scalarmuldouble
 0.1%   0.2%  26.1KiB              prek prek::cli::try_repo::try_repo::{{closure}}
 0.1%   0.2%  24.5KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::LocalHook>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.1%   0.2%  22.9KiB     granit_parser granit_parser::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  22.3KiB         [Unknown] Lp384_montjscalarmul_alt_p384_montjadd
41.9%  86.2%  11.1MiB                   And 24323 smaller methods. Use -n N to show more.
48.6% 100.0%  12.9MiB                   .text section size, the file size is 26.6MiB

Base Branch Results

 File  .text     Size             Crate Name
 1.2%   2.5% 332.0KiB        aws_lc_sys aws_lc_0_41_0_aes_gcm_encrypt_avx512
 1.2%   2.5% 332.0KiB        aws_lc_sys aws_lc_0_41_0_aes_gcm_decrypt_avx512
 0.4%   0.7%  95.4KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.7%  90.7KiB              prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.6%  85.1KiB              prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.3%   0.6%  79.4KiB             prek? <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.2%   0.4%  49.7KiB              prek prek::run::{{closure}}
 0.2%   0.4%  49.4KiB annotate_snippets annotate_snippets::renderer::render::render
 0.2%   0.3%  44.6KiB              prek prek::cli::run::run::run::{{closure}}
 0.2%   0.3%  43.9KiB             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%  32.0KiB               std core::ptr::drop_in_place<prek::languages::<impl prek::config::Language>::install::{{closure}}>
 0.1%   0.2%  31.8KiB             prek? <prek::cli::RunOptions as clap_builder::derive::Args>::augment_args
 0.1%   0.2%  29.4KiB     granit_parser granit_parser::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  28.3KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::RemoteHook>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.1%   0.2%  28.0KiB        aws_lc_sys aws_lc_0_41_0_edwards25519_scalarmuldouble_alt
 0.1%   0.2%  27.5KiB        aws_lc_sys aws_lc_0_41_0_edwards25519_scalarmuldouble
 0.1%   0.2%  26.2KiB              prek prek::cli::try_repo::try_repo::{{closure}}
 0.1%   0.2%  24.8KiB             prek? <prek::config::_::<impl serde_core::de::Deserialize for prek::config::LocalHook>::deserialize::__Visitor as serde_core::de::Visitor>::visit_map
 0.1%   0.2%  22.9KiB     granit_parser granit_parser::scanner::Scanner<T>::fetch_more_tokens
 0.1%   0.2%  22.3KiB         [Unknown] Lp384_montjscalarmul_alt_p384_montjadd
41.8%  86.0%  11.1MiB                   And 24265 smaller methods. Use -n N to show more.
48.6% 100.0%  12.9MiB                   .text section size, the file size is 26.6MiB

[prek-ci-bot]

⚡️ Hyperfine Benchmarks

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

Environment

• OS: Linux 6.17.0-1018-azure
• CPU: 4 cores
• prek version: prek 0.4.4+48 (d2a1b55 2026-06-12)
• Rust version: rustc 1.96.0 (ac68faa20 2026-05-25)
• 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	1.8 ± 0.1	1.7	2.0	1.00
prek-head --version	1.8 ± 0.1	1.7	2.2	1.02 ± 0.06

prek list

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base list	8.5 ± 0.3	8.0	9.3	1.02 ± 0.05
prek-head list	8.3 ± 0.3	7.7	8.9	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	2.6 ± 0.1	2.4	2.8	1.04 ± 0.05
prek-head validate-config .pre-commit-config.yaml	2.5 ± 0.1	2.4	2.8	1.00

prek sample-config

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base sample-config	2.1 ± 0.1	2.0	2.4	1.04 ± 0.04
prek-head sample-config	2.1 ± 0.1	2.0	2.2	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	56.3 ± 1.8	54.0	59.1	1.00 ± 0.04
prek-head run --all-files	56.2 ± 1.6	54.2	58.6	1.00

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --all-files	56.0 ± 2.0	52.3	60.4	1.01 ± 0.05
prek-head run --all-files	55.6 ± 1.6	53.3	58.6	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	55.9 ± 1.6	52.2	60.0	1.00
prek-head run --all-files	57.6 ± 3.0	53.4	73.8	1.03 ± 0.06

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	15.4 ± 0.4	14.7	16.6	1.00
prek-head run trailing-whitespace --all-files	15.8 ± 0.6	15.0	16.9	1.03 ± 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	20.5 ± 1.2	18.8	23.4	1.02 ± 0.08
prek-head run end-of-file-fixer --all-files	20.1 ± 1.0	18.1	21.7	1.00

prek run check-json --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-json --all-files	6.6 ± 0.2	6.1	7.2	1.02 ± 0.05
prek-head run check-json --all-files	6.5 ± 0.3	6.1	7.0	1.00

prek run check-yaml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-yaml --all-files	6.3 ± 0.2	6.0	6.8	1.00 ± 0.05
prek-head run check-yaml --all-files	6.3 ± 0.2	5.9	6.8	1.00

prek run check-toml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-toml --all-files	6.3 ± 0.3	5.9	7.0	1.00
prek-head run check-toml --all-files	6.9 ± 0.5	6.2	7.9	1.08 ± 0.10

prek run check-xml --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-xml --all-files	7.1 ± 1.8	5.8	12.2	1.10 ± 0.28
prek-head run check-xml --all-files	6.5 ± 0.3	6.0	7.0	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	11.6 ± 0.7	10.2	13.0	1.00
prek-head run detect-private-key --all-files	12.0 ± 0.9	10.9	14.1	1.04 ± 0.10

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	15.0 ± 0.5	14.1	16.4	1.03 ± 0.05
prek-head run fix-byte-order-marker --all-files	14.6 ± 0.5	13.5	15.7	1.00

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	3.8 ± 0.1	3.7	4.0	1.00
prek-head install-hooks	3.9 ± 0.1	3.8	4.0	1.02 ± 0.04

prek install-hooks (warm - with cache)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base install-hooks	3.8 ± 0.1	3.7	4.0	1.03 ± 0.04
prek-head install-hooks	3.7 ± 0.1	3.6	3.9	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	27.9 ± 0.8	26.7	29.2	1.00
prek-head run	29.3 ± 1.0	28.4	33.2	1.05 ± 0.05

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run --files '*.json'	6.8 ± 0.2	6.5	7.3	1.00
prek-head run --files '*.json'	7.0 ± 0.2	6.6	7.4	1.02 ± 0.04

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	6.1 ± 0.3	5.6	7.0	1.10 ± 0.06
prek-head run --dry-run --all-files	5.5 ± 0.1	5.2	5.8	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	9.2 ± 0.2	8.9	9.6	1.00
prek-head run check-hooks-apply --all-files	9.3 ± 0.3	8.9	9.8	1.01 ± 0.04

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

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run check-useless-excludes --all-files	9.3 ± 0.3	9.0	9.9	1.00
prek-head run check-useless-excludes --all-files	9.3 ± 0.4	9.0	10.2	1.01 ± 0.05

prek run identity --all-files

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
prek-base run identity --all-files	7.9 ± 0.2	7.5	8.2	1.00
prek-head run identity --all-files	8.2 ± 0.2	7.9	8.5	1.04 ± 0.03