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Backport #38788 by @terriblegoodday 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. Assisted by Claude Opus 5 and Claude Fable. Co-authored-by: Eduard Dzhumagaliev <ed_dzhumagaliev@icloud.com> Co-authored-by: silverwind <me@silverwind.io>