Fix SwifterPM handling of packages with required Git submodules

SwifterPM now correctly initializes required Git submodules when falling back to a shallow Git checkout, so packages like libwebp-Xcode that declare source folders living inside a .gitmodules entry resolve cleanly. Cached source checkouts missing submodule contents are also treated as stale and refreshed automatically on the next restore, so projects no longer get stuck on the bad cache even after tuist clean.