The project specific preferences are ignored and overridden by the workspace one

Steps to reproduce:

• Have a boolean preference key with false default value.
• Enabled this preference at workspace level by setting the value to true.
• Create a project, and the enable project specific preferences. Configure the preference value on the project to false.
• The project specific preference value will be true although I would expect false.

In the FixedScopedPreferenceStore.setValue(String, boolean); we remove the project-level preferences because it equals to the default one. Then later, when we are trying to get the value for the project specific preference, we invoke FixedScopedPreferenceStore.internalGet(String) which delegates to the PreferencesService.get(String, String, Preferences[]). Although we have the chain of preferences (starting with the project scoped one), we get the workspace level value because we have removed the preference entry from the project-level preferences earlier.

Start with FixedScopedPreferenceStore.setValue(String, boolean) and internalGet(String), then trace PreferencesService.get(String, String, Preferences[]) using the reproduction steps. Done means a project-level false value remains effective when false is the default and the workspace value is true; verify the behavior with the relevant preference tests.