chore(deps): upgrade biome to v2.4.6 and @types/bun to 1.3.10

[llbbl]

Summary

• Upgrade @biomejs/biome from 1.9.4 to 2.4.6 (major version bump)
• Upgrade @types/bun from 1.3.8 to 1.3.10 (patch)
• Run biome migrate for v2 config changes and apply v2 auto-fixes
• Update .beads/.gitignore and README for Dolt backend

Changes

Dependencies

• package.json: Bump @biomejs/biome to 2.4.6 and @types/bun to 1.3.10
• bun.lock: Updated lockfile reflecting new package versions

Biome v2 Migration

• biome.json: Apply v2 config schema changes from biome migrate
• src/commands/index.ts: Apply biome v2 auto-fixes (import sorting, unused imports/vars)
• src/lib/index.ts: Apply biome v2 auto-fixes
• src/utils/format.ts: Apply biome v2 auto-fixes
• test/utils/colors.test.ts: Apply biome v2 auto-fixes

Beads (.beads)

• .beads/.gitignore: Update ignore rules for Dolt backend
• .beads/README.md: Update documentation for Dolt backend
• .beads/metadata.json: Updated metadata
• .gitignore: Add beads backup entries
• .beads/backup/: New backup files for beads state (backup_state.json, issues.jsonl, events.jsonl, etc.)
• .beads/hooks/: New git hook scripts (post-checkout, post-merge, pre-commit, pre-push, prepare-commit-msg)

Test plan

• Run just check (lint + tests) to verify biome v2 passes cleanly
• Run just build to confirm the build succeeds
• Verify CLI behavior is unchanged with just dev --help

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