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

## 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.

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## 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

First verify that the referenced harper CLI features are released, then inspect the template deploy scripts, templates-shared/all/scripts/, and the README "## Deployment" section. Done means the deploy commands use the native CLI syntax, both obsolete JavaScript scripts are removed from the listed locations, and the README matches the new flow.

Written by the indexing model from the issue text.