feat: persist configuration across terraform interrupts

[zreigz]

Summary

Skip re-prompting on resume and flush deploy checkpoints immediately so a stop does not force the wizard to start over.

Labels

Test Plan

Checklist

• If required, I have updated the Plural documentation accordingly.
• I have added tests to cover my changes.
• I have added a meaningful title and summary to convey the impact of this PR to a user.
• I have added relevant labels to this PR to help with categorization for release notes.

[linear]

PROD-5193

[greptile-apps]

Greptile Summary

This PR persists app-domain prompt completion and deployment checkpoints so interrupted setup can resume without repeating completed work.

• Adds an explicit marker for an answered or skipped app-domain prompt.
• Flushes that marker and each successful deployment checkpoint immediately.
• Adds tests for app-domain and checkpoint persistence.
• The new persistence calls still rely on a non-atomic manifest rewrite, leaving a narrow interruption-related corruption risk.

Confidence Score: 4/5

The PR appears safe to merge, with a non-blocking hardening opportunity to make the newly frequent manifest writes atomic.

The resume markers and checkpoint ordering are persisted and tested correctly, but an interruption during the direct manifest rewrite can still corrupt the state needed for resume.

Files Needing Attention: pkg/up/deploy.go

Important Files Changed

Filename	Overview
cmd/command/up/up.go	Skips completed app-domain configuration and immediately persists both selected domains and explicit skips.
cmd/command/up/up_test.go	Covers legacy configuration detection and YAML persistence of selected or skipped app domains.
pkg/manifest/types.go	Adds the app-domain completion marker to manifest YAML and JSON serialization.
pkg/up/deploy.go	Flushes every successful checkpoint immediately, but the underlying manifest rewrite is not atomic against interruption.
pkg/up/deploy_test.go	Verifies checkpoint advancement, persistence, failure behavior, and skipping of completed phases.

_{Reviews (1): Last reviewed commit: "add comment" | Re-trigger Greptile}

[socket-security]

Review the following changes in direct dependencies. Learn more about Socket for GitHub.

Diff	Package	Supply Chain Security	Vulnerability	Quality	Maintenance	License
	google.golang.org/​grpc@​v1.82.1 ⏵ v1.83.1	+1	+16

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