java.settings.url does not override default java settings

[rgrunber]

Test.java

import java.io.Serializable;
public class Test implements Serializable {
    public void test () {
    }
}

/home/user/Scripts/org.eclipse.jdt.core.prefs (set as java.settings.url)

org.eclipse.jdt.core.compiler.problem.missingSerialVersion=error
org.eclipse.jdt.core.compiler.problem.missingJavadocComments=error
org.eclipse.jdt.core.compiler.problem.missingJavadocTags=error

On initial load, only the javadoc errors are displayed. The missingSerialVersion error is ignored (which is now the default since 0019109 ). https://github.com/eclipse/eclipse.jdt.ls/blob/master/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/managers/StandardProjectsManager.java#L262 seems to be overriding correctly, so not exactly sure where it's going wrong.

It seems to work if the settings file is project specific (.settings/org.eclipse.jdt.core.prefs).