API tooling warnings mismatch IDE vs github

[iloveeclipse]

PR validation on github reports non-existing or wrong warnings that do not match these in the IDE, see
https://github.com/eclipse-jdt/eclipse.jdt.debug/pull/428/checks?check_run_id=23798020341 for eclipse-jdt/eclipse.jdt.debug#428.

org.eclipse.jdt.debug.ui/ui/org/eclipse/jdt/debug/ui/launchConfigurations/JavaConnectTab.java
JavaConnectTab extends non-API type AbstractJavaMainTab

This shouldn't be a problem because @noextend is added on JavaConnectTab

org.eclipse.jdt.debug.ui/ui/org/eclipse/jdt/internal/debug/ui/launcher/RuntimeClasspathViewer.java
The API problem filter for: 'RuntimeClasspathViewer illegally extends TableViewer' is no longer used

There is already an API filter entry for it, and after removing the filter I get exact this warning in the IDE.

Not sure whether this is an IDE/PDE issue, github validation check issue or tycho issue...

[iloveeclipse]

Same here: https://github.com/eclipse-jdt/eclipse.jdt.ui/pull/1325/checks?check_run_id=23801196290.
Lot of API warnings that aren't shown in IDE.
Could this be some side effect of missing system packages (#1227)?