Ensure all Java-side usages of config flags are using Java flags

Previously we were using native config flags in some places that expected
Java flags, and vice-versa. All usages of config flags are now annotated
to ensure we're using the right type.

Cleans up annotations on most methods that were touched.

Bug: 21161798
Change-Id: Ifd87dfb12199fc8258915d8a510e03ddb681ca89