The project preference should only persist non default values

[jdneo]

The code https://github.com/eclipse/eclipse.jdt.ls/blob/f6af5170ea2f63dd2864ab2e73beb84154163b98/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/preferences/Preferences.java#L2051 sets the whole set of the Java Core options to the project preferences file, which introduce a side effect that in the future when we want to change a value in the global preferences, it will not take effect since the project level preference will always override it.

We should only persist the key-values which are not equal to the default ones.