Currently setPubRootDirectories replaces the entire set of pubRoot Directories. So the caller can run into race conditions where another caller has changed the pubroot directories, since the last time getPubRootDirectories were called.

To allow for more flexible and safe interaction with pubRootDirectories, change the API to have addPubRootDirectories(List<String>) and removePubRootDirectories(List<String>).

Then change setPubRootDirectories so that it actually wraps addPubRootDirectories and add a deprecation notice to the function