Fix onboarding hooks step to use prek instead of pre-commit

[Miyamura80]

Summary

• Updated onboard.py hooks step (step 4/6) to read prek.toml instead of .pre-commit-config.yaml
• Replaced yaml import with stdlib tomllib for TOML parsing
• Changed install command from uv run pre-commit install to prek install
• Removed pre-commit from dev dependencies in pyproject.toml

Test plan

• Run make onboard and verify step 4 (Hooks) no longer errors with ".pre-commit-config.yaml not found"
• Verify the hooks table displays all hooks from prek.toml
• Verify prek install is invoked when activating hooks

🤖 Generated with Claude Code

[greptile-apps]

Greptile Summary

Migrated the onboarding hooks step from pre-commit to prek by switching from YAML to TOML parsing and updating the install command to use uv tool run prek install.

• Replaced yaml import with stdlib tomllib for parsing prek.toml instead of .pre-commit-config.yaml
• Changed install command from uv run pre-commit install to uv tool run prek install (properly addresses previous review comment about prek availability)
• Removed redundant pre-commit>=4.5.1 from dev dependencies (PyYAML remains in main dependencies for other uses)
• Updated all user-facing text references from "pre-commit" to "prek"
• Parsing logic remains identical since prek.toml uses the same structure as pre-commit-config.yaml

Confidence Score: 5/5

• This PR is safe to merge with minimal risk
• The changes are straightforward and well-executed: replaces deprecated yaml parsing with stdlib tomllib, correctly updates command to use uv tool run prek install (addressing the previous review concern), and properly removes only the redundant pre-commit dependency while keeping PyYAML for other uses. The parsing logic is unchanged and correct for the prek.toml structure.
• No files require special attention

Important Files Changed

Filename	Overview
onboard.py	Replaced yaml with tomllib for parsing prek.toml, updated command to use uv tool run prek install
pyproject.toml	Removed redundant pre-commit from dev dependencies (PyYAML remains in main dependencies)
uv.lock	Lockfile updated to remove pre-commit and its dependencies (cfgv, distlib, identify, nodeenv, virtualenv)

_{Last reviewed commit: 4674c7c}

[greptile-apps]

_{3 files reviewed, 1 comment}

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