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This is a regression in the behavior. When the debugger is started and the sources are not yet fully scanned, the action just blocks in AWT and waits for the scan to finish. This blocks all UI and NetBeans are not responsive until the scan finishes. There was a dialog notifying about the necessity to wait for the scan in the past.
Created attachment 36687 [details] The full thread dump.
Requires the new API like runWhenScannedFinished (Runnable). There are already SourceUtils.isScanInProgress () and SourceUtils.waitScanFinished().
If you have a task which need to be done when scan is done use JavaSource.runWhenScanFinished(). Checking in apichanges.xml; /cvs/java/source/apichanges.xml,v <-- apichanges.xml new revision: 1.8; previous revision: 1.7 done Checking in nbproject/project.properties; /cvs/java/source/nbproject/project.properties,v <-- project.properties new revision: 1.18; previous revision: 1.17 done Checking in src/org/netbeans/api/java/source/JavaSource.java; /cvs/java/source/src/org/netbeans/api/java/source/JavaSource.java,v <-- JavaSource.java new revision: 1.45; previous revision: 1.44 done Checking in src/org/netbeans/modules/java/source/classpath/GlobalSourcePath.java; /cvs/java/source/src/org/netbeans/modules/java/source/classpath/GlobalSourcePath.java,v <-- GlobalSourcePath.java new revision: 1.8; previous revision: 1.7 done Checking in src/org/netbeans/modules/java/source/usages/RepositoryUpdater.java; /cvs/java/source/src/org/netbeans/modules/java/source/usages/RepositoryUpdater.java,v <-- RepositoryUpdater.java new revision: 1.49; previous revision: 1.48 done Checking in test/unit/src/org/netbeans/api/java/source/JavaSourceTest.java; /cvs/java/source/test/unit/src/org/netbeans/api/java/source/JavaSourceTest.java,v <-- JavaSourceTest.java new revision: 1.11; previous revision: 1.10 done