chore: migrate legacy pre-commit hook to .pre-commit-config.yaml

Replaces shell script (.git/hooks/pre-commit.legacy) with ecosystem-managed pre-commit framework:
- gitleaks/gitleaks: secret scanning
- jumanjihouse/pre-commit-hooks: shellcheck wrapper
- pre-commit/pre-commit-hooks: JSON/YAML validation, end-of-file-fixer, trailing-whitespace
- local hooks: SKILL.md frontmatter validation

Uses pinned versions for reproducibility across environments. Includes auto-fixes from hook runs (formatting, trailing whitespace, JSON beautification).

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

.gitignore

@@ -24,6 +24,3 @@ node_modules/
 
 # Claude Code local settings (machine-specific)
 .claude/settings.local.json
-
-graphify-out/cost.json        # local only
-graphify-out/cache/         # optional: commit for speed, skip to keep repo small