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 access the settings programmatically?
Source : Eclipse wiki
If you want to keep preferences from one version to the other, export them using File/Export/Preferences.
Preferences are stored in various places (this applies to Eclipse 3.1)
for each installation (but this may vary for multi-user installations), in files stored in:
There is typically one file per plugin, with a prefs extension. Note that very few plug-ins use installation-wide preferences.
for each workspace, in files stored in
There is typically one file per plugin, with a prefs extension. for each project --for project-level settings -- in files stored in a .settings sub-directory of your project folder.
Here's the article to access preferences using java code.