Fix SwiftPM registry duplicate manifest variants blocking installs

The cache registry now deduplicates Swift package manifest variants that resolve to the same Swift tools version, so tuist install and tuist generate no longer abort with “duplicate key found: ‘Package@swift-X.Y.Z.swift’” errors during SwiftPM registry resolution. Fresh worktrees (including those used by automated agents) can complete dependency installation, generate the workspace, and run focused CLI builds and tests.