Where does Eclipse store preferences?

Question

When I change a setting in a window like in the screenshot below, where are those settings actually stored?

Bonus: Is there any way, using Java, Eclipse RCP etc, to

Answer 1

You can see most of the relevant eclipse settings (mainly for JDT) in the saneclipse project from Lars Vogel.

See the vogellacompany/com.vogella.saneclipse repo, which will tweak and fine-tune the settings of:

com.vogella.saneclipse.preferences/.settings/org.eclipse.jdt.core.prefs
com.vogella.saneclipse.preferences/.settings/org.eclipse.core.runtime.prefs
com.vogella.saneclipse.preferences/.settings/org.eclipse.core.resources.prefs
com.vogella.saneclipse.templates/.settings/org.eclipse.jdt.core.prefs
com.vogella.saneclipse.fileextensions/.settings/org.eclipse.jdt.core.prefs
com.vogella.saneclipse.fileextensions/.settings/org.eclipse.pde.core.prefs