chore: reclassify @koi/cli from L3 to L2 (application layer)

[windoliver]

Problem

@koi/cli is classified as L3 in scripts/layers.ts but contains 5,661 LOC with a full CLI application: arg parsing, 5+ commands, bootstrap logic. It violates the L3 "no new logic" rule.

Fix

1. Move @koi/cli from the L3_PACKAGES set in scripts/layers.ts
2. Update CLAUDE.md L3 list to remove @koi/cli

Files

• scripts/layers.ts line 64
• CLAUDE.md (L3 packages list)

Verification

• Run bun run check-layers after the change