Nested `Package.swift` files overwrote the real package manifest. The
parser matched on the base name and kept the last entry in ZIP order.
`apple/swift-collections` ships `Benchmarks/Package.swift` and
`Utils/Debugger/FormatterFixtures/Package.swift`. The latter sorts after
the root `Package.swift`, so the registry stored a fixture manifest with
the wrong `swift-tools-version`, causing a toolchain mismatch and a
failed build. GRDB, swift-markdown, swift-syntax, sentry-cocoa and
SDWebImage share this layout.
The parser now keeps only manifests from the shallowest directory
holding one. That covers both a package at the archive root and the
single top level directory `swift package archive-source` produces. At
equal depth the first directory by name wins, so an archive always
yields the same metadata.
A nested manifest above the size limit no longer rejects the upload.
Co-authored-by: silverwind <me@silverwind.io>
