Make archives and native installers effectively incremental

[mthalman]

Part of #48070. Make archive, Windows MSI/bundle, and macOS PKG/product-archive incrementality effective after their upstream layouts are stable. Complete existing input sets so every consumed layout, authoring file, executable, and generated manifest invalidates the correct output, and split work into platform-specific PRs.

Depends on: #55868, #55869, #55870, #55871, #55872, #55873, and #55874.