Having submodules inside subtrees breaks submodule update.

Bug: b/140546382
Change-Id: I0e3e9591bfd1aa8813d1e8764f702d87c5ac5e84
Reviewed-on: https://swiftshader-review.googlesource.com/c/SwiftShader/+/36030
Kokoro-Presubmit: kokoro <noreply+kokoro@google.com>
Reviewed-by: Nicolas Capens <nicolascapens@google.com>
Tested-by: Ben Clayton <bclayton@google.com>