[codex] fix unordered application command arrays

[valipuha]

Summary

• treat integration_types and contexts as unordered sets when computing application command differences
• avoid unnecessary command updates when the same values are provided in a different order
• add regression coverage for both unsorted array cases

Root cause

The command diff logic compared integration_types and contexts positionally, so semantically equivalent arrays with a different order were reported as changes.

Validation

• corepack yarn vitest run tests/application-commands/computeDifferences.test.ts
• corepack yarn typecheck

Fixes #865.