Fix duplicate SwiftPM manifest variants in registry resolution

The cache registry now deduplicates Swift package manifest variants by their canonical Swift tools version. When a package’s default Package.swift and an alternate Package@swift-X.Y.swift resolve to the same Swift tools version, the registry keeps only the default manifest and no longer advertises or persists the redundant alternate. This prevents SwiftPM from failing with duplicate key found errors during dependency resolution, so fresh worktrees can run tuist install, generate the workspace, and build or test focused targets without getting blocked before the workspace is created.