Partition overridden Metro cache roots by app

[janicduplessis]

Description

STIM_CLI_METRO_CACHE and machine-level caches.metroCache currently bypass the app-name segment, causing configured roots to become one flat Metro store. This makes per-app reporting and pruning impossible.

Closes #75.

Solution

• Treat both Metro overrides as parent roots and append the same sanitized app name used by the default layout.
• Keep environment, machine-config, and default resolution aligned across @stim-cli/core, @stim-cli/metro, and the CLI's bare and Expo start paths.
• New named registrations carry a versioned metro-named-v1 layout marker. They replace only an exact unmarked legacy flat Metro record; if an older package registers that parent afterward, current gc suppresses it only when a marked child proves the migration. Marked stores are preserved when they later become another override parent and remain visible but report-only while a marked child exists. Canonical and symlinked child relationships are handled safely. Existing root-level files are left untouched for manual cleanup.
• Document the new contract and migration in the package docs, shipped skill, and guide.

Test plan

• Cover default, machine-config, environment-precedence, relative-config rejection, and name-sanitization contracts.
• Verify standalone and CLI layout markers, marked/unmarked replacement, both mixed-version registration orders, nested current parent/child discovery, real and symlinked-child gc --delete --older-than safety, and unrelated same-root/ancestor preservation.
• Run pnpm run format:check, pnpm run lint, pnpm run build, pnpm run typecheck, pnpm run knip, pnpm run test:runtime, and pnpm test (2,273 passing).
• Run pnpm run test:e2e (12 passing).
• Run all four native cache harness variants with --dry-run; no full native device build was performed.