Replace pre-commit with prek

[Miyamura80]

Replaced pre-commit with prek as requested. This includes:

• Adding prek to pyproject.toml dev dependencies.
• Creating prek.toml with the same hooks as .pre-commit-config.yaml.
• Removing .pre-commit-config.yaml.
• Updating Makefile setup_githooks and install_tools targets to use prek.
• Adding documentation for prek in .claude/skills/prek/SKILL.md.

Verified by running prek run --all-files which passed all checks.
Note: make ci fails due to pre-existing type errors in utils/llm/dspy_langfuse.py, unrelated to these changes.

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PR created automatically by Jules for task 5576607088466303257 started by @Miyamura80

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[greptile-apps]

Greptile Summary

This PR successfully replaces pre-commit with prek as a faster, Rust-based alternative for managing git hooks. All hooks from .pre-commit-config.yaml were correctly migrated to prek.toml with identical configuration. The changes include:

• Added prek>=0.3.3 to dev dependencies in pyproject.toml
• Created prek.toml with all 8 hooks (check-added-large-files, lint-links, make-fmt, ruff-check, ruff-complexity, ruff-tech-debt, pylint-duplicate-code, ai-writing-check)
• Updated Makefile targets (setup_githooks and install_tools) to use prek install and uv tool install prek
• Removed .pre-commit-config.yaml
• Added comprehensive documentation in .claude/skills/prek-precommit-hook/SKILL.md

The migration is complete and validated by the author running prek run --all-files successfully.

Confidence Score: 5/5

• This PR is safe to merge with no risk
• Clean migration from pre-commit to prek with complete feature parity. All 8 hooks preserved with identical configuration, Makefile properly updated, dependency correctly added, and documentation provided. Author verified functionality by running prek successfully. No logic changes, security concerns, or breaking changes.
• No files require special attention

Important Files Changed

Filename	Overview
.claude/skills/prek-precommit-hook/SKILL.md	New skill documentation added for prek usage and commands
Makefile	Updated setup_githooks and install_tools targets to use prek instead of pre-commit
prek.toml	New prek configuration with same hooks as previous pre-commit setup
pyproject.toml	Added prek>=0.3.3 to dev dependencies

_{Last reviewed commit: 112d883}