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Fix getwithbase() to drop base keys when there is a setting value (#6912)#7001
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Resolves#6912
Fixes code in Settings.getwithbase() to drop base keys when the setting value already has them.
Logs a warning in getwithbase() when duplicate keys are detected (e.g., both "foo.Foo" and Foo present).
Test getwithbase() resolves duplicate keys when merging base and custom settings.