Replace System.err with Messages.showWarning #356

Job	Run time
Test Processing	2m 52s
(macos/x64) Create Processing Build	7m 13s
(linux/aarch64) Create Processing Build	7m 44s
(linux/x64) Create Processing Build	9m 45s
(macos/aarch64) Create Processing Build	3m 29s
(windows/x64) Create Processing Build	5m 8s
	36m 11s

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