The project's package fragments are not update to date when adding a new one.

[jdneo]

Repro steps:

• Open a java project to let the Java Language Server start up
• Create a new folder, the folder path is belong to one of the project's PackageFragmentRoot
• Create a Java file in that folder
• Then, when we get a IJavaProject instance in the Java side, and inspect the PackageFragment, there is no entry for the new created one. (You can call project.getPackageFragmentRoots() first, after find the right root, call getChildren() over it)

This bug affects several scenario, like:

• Cannot move a compilation unit to a newly created package (gif above)
• Could not find or load main class xxx when debugging a main class in newly created package
• Java dependency viewer cannot show the newly created package and its members in the explorer
• Java Test explorer cannot show the newly created package and its members in the explorer

[jdneo]

@snjeza @fbricon

I found a reason which may cause this bug. In https://github.com/eclipse/eclipse.jdt.ls/blob/ff78ddaf41417aec47cfdf1aa619a96f87462f61/org.eclipse.jdt.ls.core/src/org/eclipse/jdt/ls/core/internal/JDTUtils.java#L894

We always refresh the parent with zero depth. After this operation, the parent of the newly created package is still not aware of the existence of its new member. Maybe we need to use DEPTH_ONE here?

[fbricon]

If that's what it takes to work then ok