Fix stale E2E CLI assumptions

[isaacroldan]

What changed

• Updates the E2E deployApp helper to pass --allow-updates by default instead of the removed --force flag.
• Removes the PTY smoke test's hard-coded wait for CLI version output containing 3.. The test still asserts the command exits successfully and emits semver output.

Why

Recent PR and merge-queue runs are green at the workflow level but E2E jobs are failing because e2e-tests has continue-on-error: true.

The current job-level failures are stale test assumptions:

• Shard 1: tests/app-deploy.spec.ts fails at deploy step 2 with Nonexistent flag: --force.
• Shard 2: tests/smoke-pty.spec.ts fails waiting for output 3. while the CLI now prints 4.0.0.

Validation

• git diff --check
• pnpm --filter @shopify/e2e type-check
• pnpm --filter @shopify/e2e lint

I did not run the full E2E suite locally because it depends on CI secrets and live Shopify test resources.

[Copilot]

Pull request overview

This PR updates the E2E test suite to match current Shopify CLI behavior by removing assumptions about deprecated flags and a hard-coded major version.

Changes:

• Update the E2E deployApp helper to pass --allow-updates by default (replacing removed --force).
• Make the PTY smoke test version assertion major-version-agnostic by removing the wait for output containing 3. while still asserting successful exit and semver output.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
packages/e2e/tests/smoke-pty.spec.ts	Removes the hard-coded wait for 3. output and keeps a generic semver assertion after the command exits.
packages/e2e/setup/app.ts	Replaces the deprecated force option/flag with allowUpdates (defaulting true) and adds allowDeletes support.

---

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[gonzaloriestra]

You can find the instructions to run the tests locally here: https://vault.shopify.io/teams/2238-DevTools/docs/dev-platform/cli/Testing#how-to-run-e2e-tests

They are failing for me:

Error: posix_spawnp failed.

   at ../setup/global-auth.ts:81

  79 |   spawnEnv.CODESPACES = 'true'
  80 |
> 81 |   const ptyProcess = nodePty.spawn('node', [executables.cli, 'auth', 'login'], {
     |                              ^
  82 |     name: 'xterm-color',
  83 |     cols: 120,
  84 |     rows: 30,
    at UnixTerminal (/Users/gonzalo/src/github.com/Shopify/cli/node_modules/.pnpm/node-pty@1.1.0/node_modules/node-pty/src/unixTerminal.ts:106:22)
    at Module.spawn (/Users/gonzalo/src/github.com/Shopify/cli/node_modules/.pnpm/node-pty@1.1.0/node_modules/node-pty/src/index.ts:31:10)
    at globalSetup (/Users/gonzalo/src/github.com/Shopify/cli/packages/e2e/setup/global-auth.ts:81:30)

/Users/gonzalo/src/github.com/Shopify/cli/packages/e2e:
 ERR_PNPM_RECURSIVE_EXEC_FIRST_FAIL  Command failed with exit code 1: playwright test
 ELIFECYCLE  Command failed with exit code 1.

Anyway, the changes here make total sense.