Swap template deploy scripts to native `harper` CLI once by_ref ships

[dawsontoth]

Context

Templates currently ship scripts/deploy.mjs + scripts/setup-deploy.mjs to do deploy-by-reference, because the released harper CLI doesn't yet have native support.

Action (once released)

When harper deploy by_ref=true (HarperFast/harper#1777), add_ssh_key generate=true (HarperFast/harper-pro#570), and harper deploy --setup (HarperFast/harper#1778) land in a released harper:

• change the template deploy script to harper deploy by_ref=true restart=true replicated=true,
• change deploy:setup to harper deploy --setup,
• delete scripts/deploy.mjs and scripts/setup-deploy.mjs (also from templates-shared/all/scripts/),
• update the README "## Deployment" section accordingly.

Part of the deploy-by-reference effort.

---

Related — deploy-by-reference effort

• HarperFast/harper#1849 — two-phase stage/activate + revert_component
• HarperFast/harper#1850 — harper deploy by_ref=true (deploy by git reference)
• HarperFast/harper#1851 — harper deploy setup=true (client-side sealed deploy credential)
• HarperFast/harper#1876 — CI token auth + harper login --for-ci
• HarperFast/harper-pro#594 — add_ssh_key generate=true (cluster-side keygen)
• HarperFast/create-harper#118 — scaffolds this flow
• HarperFast/documentation#599 — two-phase deploy docs
• HarperFast/documentation#616 — by-reference / sealed-credential / CI-auth docs