Source.java is a non-project file, only syntax errors are reported
@fbricon We have only one single file Source.java. How to supress or resolve this?

Can you try adding "java.errors.incompleteClasspath.severity": "ignore" to your settings?
Still it is coming
@GNSubrahmanyam what happens if you click on the quick fix, on the diagnostic marker?
@testforstephen @jdneo @Eskibear did we break "java.errors.incompleteClasspath.severity": "ignore" with the syntax server mechanism?
Error: Command 'java.project.refreshDiagnostics' not found
did we break "java.errors.incompleteClasspath.severity": "ignore" with the syntax server mechanism?
Previously this setting is used to control whether to display a notification message box for classpath incomplete, it's useful. When we discard the message box and display the non-project file as a warning diagnostics, since the PROBLEMS view is less disturbing, the new UX won't consume that setting.
@testforstephen In which version you introduced this? and any alternative way to ignore that.
@testforstephen any updates ?
The PR https://github.com/eclipse/eclipse.jdt.ls/pull/1366 added this. No setting to turn it off.
@testforstephen What does "java.errors.incompleteClasspath.severity": "ignore" do
I am using this via eglot package of emacs. Getting the same problem.
The per project workspace folder is generated and whenever I open a Java file from the project, a corresponding class file is also generated inside workspace/jdt.ls-java-project also. But still the editor reports this,
Java [16]: FileName.java is a non-project file, only syntax errors are reported