If anyone comes looking, the issue is related to the AWS Codebuild feature to cache the source.
LOCAL_SOURCE_CACHE should be disabled.
LOCAL_SOURCE_CACHE
Caches Git metadata for primary and secondary sources.
After the cache is created, subsequent builds pull only the change between commits. T
his mode is a good choice for projects with a clean working directory and a source that is a large Git repository.
If you choose this option and your project does not use a Git repository (GitHub, GitHub Enterprise, or Bitbucket), the option is ignored.