Fix Claude alert changes not applying immediately

[mylee04]

Summary

• apply cn alerts add, remove, and reset changes immediately when Claude hooks are already enabled
• repair stale Claude notification matchers when an already-enabled alert type is added again
• add regression coverage and update the README behavior notes

Root cause

Alert commands updated the persisted alert-type list but left the installed Claude Notification matcher unchanged until the user ran cn on again. The README examples did not make that extra step clear, so permission prompt alerts appeared enabled while the active hook still matched only idle_prompt.

Validation

• ./scripts/run_tests.sh — 28/28 passed
• Bash syntax checks passed through the test runner
• make lint could not run because shellcheck is not installed locally

Fixes #57