Suppress deprecation and removal warnings of internal methods

There are a few places in JavaFX where we use public JavaFX API that has been deprecated or deprecated for removal. Since there is no problem with using these methods internally, we should add the appropriate `@SuppressWarnings` annotation where needed to make the build less noisy.

I have attached a pair of log files generated by running:

gradle --info -PLINT="deprecation,removal"

The first file is the list of [deprecation] warnings and the second is the list of [removal] warnings.

Note that included in the list of deprecation warnings is a use of the deprecated newInstance method from java.base. These will be addressed separately, by using a replacement API, rather than suppressing the warnings.