Remove rewriteConfiguration from write path to fix config2.map crash

[lizkenyon]

Summary

Fixes shop/issues#8553 — config2.map is not a function
Vault issue: https://vault.shopify.io/issues/8435

Stops using rewriteConfiguration in writeAppConfigurationFile and replaces it with a simple stripEmptyObjects utility. The Zod schema walk was the root cause of the crash. rewriteConfiguration is kept exported for its other consumer (breakdown-extensions.ts), which is untouched in this PR.

Root Cause

When loadOpaqueApp (#6751) can't Zod-validate a local TOML config (e.g., a third-party template without client_id), it falls back to raw, unvalidated TOML data. This raw data is deep-merged with the remote config and passed to writeAppConfigurationFile, where rewriteConfiguration walked the Zod schema assuming config values matched schema types — calling .map() on non-arrays and Object.entries() on non-objects.

Triggered by app dev --reset (or any link flow) on apps using third-party templates.

Why remove instead of guard

• Defensive guards are an infinite game of catching arbitrary type mismatches
• Pass-through of invalid data causes downstream bugs (e.g., writing a config without client_id makes the app appear "unlinked")
• rewriteConfiguration's only meaningful behaviors were key reordering (cosmetic) and empty-object stripping — only the latter is needed
• A longer-term improvement would be to use TomlFile.patch() for surgical edits that preserve comments/formatting

Changes

• write-app-configuration-file.ts: Stop calling rewriteConfiguration in writeAppConfigurationFile. Add stripEmptyObjects utility. Add structuredClone to prevent mutating the caller's config (previously masked by rewriteConfiguration creating fresh objects). Add Array.isArray guard in condenseComplianceAndNonComplianceWebhooks. Keep rewriteConfiguration exported for breakdown-extensions.ts.
• link.ts: Remove schema from writeAppConfigurationFile call and getAppVersionedSchema import.
• Tests: Update all callers. Add stripEmptyObjects tests. Add type-mismatched data crash test. Convert link.test.ts TOML comparisons to snapshots. Update round-trip stability tests to 3-write pattern. Update 2 configuration object expectations to reflect that write-time mutations (webhook condensation, URI relativization) no longer leak back to the caller.

Behavior change

Key ordering in the generated TOML now follows JS object insertion order rather than schema declaration order. This may cause a one-time key reorder in shopify.app.toml on the next app link or app config pull. Subsequent writes are stable.

Not changed

• breakdown-extensions.ts — still uses rewriteConfiguration for config diffing. Its inputs come from the platform API and Zod-parsed config (not the raw TOML fallback), so it does not have the same crash risk.

Test plan

• stripEmptyObjects unit tests
• writeAppConfigurationFile tests (comments, empty entries, empty arrays, type-mismatched data)
• Config pipeline snapshot tests regenerated
• Link tests pass (23/23)
• Breakdown extensions tests pass without changes (25/25)
• Manual: shopify app init with a template lacking client_id, then shopify app dev --reset — should not crash

🤖 Generated with Claude Code

[lizkenyon]

• Remove rewriteConfiguration from write path to fix config2.map crash #7131 👈 (View in Graphite)
• main

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[Copilot]

Pull request overview

This PR hardens rewriteConfiguration so it can safely reorder keys even when it receives nullish or type-mismatched config data (e.g., raw TOML fallback from third-party templates), preventing crashes like config2.map is not a function during app config writes.

Changes:

• Add early null/undefined guards in rewriteConfiguration, plus Array.isArray and typeof === 'object' checks before array/object traversal.
• Add unit tests covering null/undefined and type-mismatched values (including a case using the real buildVersionedAppSchema()).
• Add a patch changeset documenting the crash fix.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
packages/app/src/cli/services/app/write-app-configuration-file.ts	Adds defensive guards in rewriteConfiguration to avoid .map()/Object.entries() on invalid shapes.
packages/app/src/cli/services/app/write-app-configuration-file.test.ts	Adds focused tests to ensure rewriteConfiguration doesn’t throw on nullish/type-mismatched config.
.changeset/chilly-glasses-fetch.md	Records a patch release note for the crash fix.

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[alfonso-noriega]

Minor comment that needs addressing, everything else looks great!

[alfonso-noriega]

Normally we do not add changesets for non user facing changes, but if it is meant to be trigger a patch, we are only generating changesets on the PR against the stable branch to force the new version generation