Fallback to manual stage for hooks specified directly in command line

[drainpixie]

Closes #1177. I'm aware right now the PR lacks documentation and test changes; I wanted to get a code review first to ensure my approach is correct as it's my first time with this codebase. I have tested the current changes manually as such:

~/p/o/testing main (nix) $ cat .pre-commit-config.yaml
repos:
  - repo: local
    hooks:
      - id:  foo
        name: Foo 
        entry: echo "foo"
        language: system
        stages: [commit]

      - id: bar 
        name: Bar 
        entry: echo "Bar"
        language: system
        stages: [manual]

      - id: baz
        name: Baz
        entry: echo "Baz"
        language: system
        stages: [manual]

~/p/o/testing main (nix) $ prek    
Foo..................................................(no files to check)Skipped
~/p/o/testing main (nix) $ prek bar
error: No hooks found for stage `pre-commit` after filtering
~/p/o/testing main (nix) $ ../prek/target/debug/prek
Foo..................................................(no files to check)Skipped
~/p/o/testing main (nix) $ ../prek/target/debug/prek bar
warning: No hooks found for stage `pre-commit` after filtering; running with `--hook-stage manual --all-files` as the selected hook(s) support the `manual` stage.
Bar......................................................................Passed
~/p/o/testing main (nix) $ ../prek/target/debug/prek bar baz
warning: No hooks found for stage `pre-commit` after filtering; running with `--hook-stage manual --all-files` as the selected hook(s) support the `manual` stage.
Bar......................................................................Passed
Baz......................................................................Passed
~/p/o/testing main (nix) $ 

[potiuk]

I think the interesting cases to add also as manual tests are :

• ~/p/o/testing main (nix) $ ../prek/target/debug/prek foo -> should work in commit mode
• ~/p/o/testing main (nix) $ ../prek/target/debug/prek foo bar baz (should we only run foo, or foo as commit and bar/bas as manual or fail whole command)

[codecov]

Codecov Report

❌ Patch coverage is 97.05882% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 89.74%. Comparing base (b5be7c6) to head (d1d8179).
⚠️ Report is 7 commits behind head on master.

Files with missing lines	Patch %	Lines
src/cli/run/selector.rs	85.71%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1185   +/-   ##
=======================================
  Coverage   89.73%   89.74%           
=======================================
  Files          78       78           
  Lines       14767    14796   +29     
=======================================
+ Hits        13251    13278   +27     
- Misses       1516     1518    +2     

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[github-actions]

📦 Cargo Bloat Comparison

Binary size change: +0.00% (16.7 MiB → 16.7 MiB)

Expand for cargo-bloat output

Head Branch Results

 File  .text     Size          Crate Name
 0.6%   1.3% 104.8KiB          prek? <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.6%   1.3% 100.4KiB           prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.7%  54.6KiB           prek prek::archive::unpack::{{closure}}
 0.3%   0.7%  53.0KiB             h2 h2::proto::connection::Connection<T,P,B>::poll
 0.3%   0.6%  48.6KiB           prek prek::run::{{closure}}
 0.2%   0.5%  40.0KiB           prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.2%   0.5%  39.1KiB          prek? <prek::cli::RunArgs as clap_builder::derive::Args>::augment_args
 0.2%   0.5%  37.3KiB regex_automata regex_automata::meta::strategy::new
 0.2%   0.4%  35.2KiB           prek prek::workspace::Workspace::discover
 0.2%   0.4%  31.4KiB           std? <core::marker::PhantomData<T> as serde_core::de::DeserializeSeed>::deserialize
 0.2%   0.4%  30.4KiB           prek prek::cli::run::run::run::{{closure}}
 0.2%   0.4%  28.8KiB           prek prek::languages::node::installer::NodeInstaller::install::{{closure}}
 0.2%   0.4%  28.1KiB             h2 h2::proto::connection::DynConnection<B>::recv_frame
 0.2%   0.3%  27.6KiB           prek prek::identify::by_extension::{{closure}}
 0.1%   0.3%  25.1KiB           prek prek::main
 0.1%   0.3%  24.4KiB     hyper_util hyper_util::client::legacy::client::Client<C,B>::send_request::{{closure}}
 0.1%   0.3%  24.4KiB           std? <core::marker::PhantomData<T> as serde_core::de::DeserializeSeed>::deserialize
 0.1%   0.3%  24.3KiB     hyper_util hyper_util::client::legacy::client::Client<C,B>::connect_to::{{closure}}::{{closure}}::{{closure}}
 0.1%   0.3%  24.2KiB           prek prek::hook::HookBuilder::build::{{closure}}
 0.1%   0.3%  23.9KiB          hyper hyper::proto::h1::dispatch::Dispatcher<D,Bs,I,T>::poll_loop
41.1%  88.8%   6.8MiB                And 10630 smaller methods. Use -n N to show more.
46.3% 100.0%   7.7MiB                .text section size, the file size is 16.7MiB

Base Branch Results

 File  .text     Size          Crate Name
 0.6%   1.3% 104.8KiB          prek? <prek::cli::Command as clap_builder::derive::Subcommand>::augment_subcommands
 0.6%   1.3% 100.4KiB           prek prek::languages::<impl prek::config::Language>::run::{{closure}}::{{closure}}
 0.3%   0.7%  54.6KiB           prek prek::archive::unpack::{{closure}}
 0.3%   0.7%  53.0KiB             h2 h2::proto::connection::Connection<T,P,B>::poll
 0.3%   0.6%  48.6KiB           prek prek::run::{{closure}}
 0.2%   0.5%  40.0KiB           prek prek::languages::<impl prek::config::Language>::install::{{closure}}
 0.2%   0.5%  39.2KiB          prek? <prek::cli::RunArgs as clap_builder::derive::Args>::augment_args
 0.2%   0.5%  37.3KiB regex_automata regex_automata::meta::strategy::new
 0.2%   0.4%  35.2KiB           prek prek::workspace::Workspace::discover
 0.2%   0.4%  31.4KiB           std? <core::marker::PhantomData<T> as serde_core::de::DeserializeSeed>::deserialize
 0.2%   0.4%  30.1KiB           prek prek::cli::run::run::run::{{closure}}
 0.2%   0.4%  28.8KiB           prek prek::languages::node::installer::NodeInstaller::install::{{closure}}
 0.2%   0.4%  28.1KiB             h2 h2::proto::connection::DynConnection<B>::recv_frame
 0.2%   0.3%  27.6KiB           prek prek::identify::by_extension::{{closure}}
 0.1%   0.3%  25.1KiB           prek prek::main
 0.1%   0.3%  24.4KiB     hyper_util hyper_util::client::legacy::client::Client<C,B>::send_request::{{closure}}
 0.1%   0.3%  24.4KiB           std? <core::marker::PhantomData<T> as serde_core::de::DeserializeSeed>::deserialize
 0.1%   0.3%  24.3KiB     hyper_util hyper_util::client::legacy::client::Client<C,B>::connect_to::{{closure}}::{{closure}}::{{closure}}
 0.1%   0.3%  24.2KiB           prek prek::hook::HookBuilder::build::{{closure}}
 0.1%   0.3%  23.9KiB          hyper hyper::proto::h1::dispatch::Dispatcher<D,Bs,I,T>::poll_loop
41.1%  88.8%   6.8MiB                And 10633 smaller methods. Use -n N to show more.
46.3% 100.0%   7.7MiB                .text section size, the file size is 16.7MiB

[j178]

Thank! I removed the extra fallback to --all-files and kept only the manual-stage fallback. --all-files controls file selection, which is orthogonal to hook stages, so letting the stage toggle alter file discovery was confusing. Keeping the fallback scoped to manual makes the behavior easier to reason about without surprising changes to the file filter logic.

[drainpixie]

Glad I could help :)