refactor(spm): collapse helpers, trim verbose comments

Audit-driven cleanup across setup-apple-spm.js, generate-spm-xcodeproj.js,
and spm-utils.js. No behavior changes; 245/245 tests pass.

- Inline describeRnRootMismatch → formatRnRootMismatchMessage used only by
  the clean-refuse path; drop the duplicate test block.
- Extract promptYesNo(question, defaultYes) — collapses four near-identical
  readline + TTY-guard + Y/n implementations.
- Extract listSpmXcodeprojs(appRoot) — one readdirSync + filter shared by
  findExistingSpmXcodeproj and gatherCleanTargets.
- Inline loadAutolinkingConfig and generateAutolinkingPackage (one-call
  wrappers).
- Replace uniquePackages manual dedupe loop with Array.from(new Map(...)).
- Split runCodegenAndInstallTemplate into installSpmCodegenTemplate +
  the combo; runCodegenStep now delegates instead of duplicating the body.
- Trim docstrings that restated WHAT (gatherCleanTargets,
  decideLegacyMigration, SPM_MANAGED_MARKER) and remove the no-op
  "backward compat" block.

Net: -189 lines across 4 files. Flow / ESLint / Prettier clean.

Author: chrfalch