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This bug was originally marked as duplicate of bug 194810, that is already resolved. This bug is still valid, so this seems to be another bug, but it might be related. Build: NetBeans IDE 7.3 Beta 2 (Build 201211062253) VM: Java HotSpot(TM) 64-Bit Server VM, 23.5-b02, Java(TM) SE Runtime Environment, 1.7.0_09-b05 OS: Windows 7 User Comments: GUEST: Not sure what happened but the background scanning is removing file from my project. Stacktrace: java.lang.Exception: Scan canceled. at java.lang.Thread.getStackTrace(Thread.java:1567) at org.netbeans.modules.parsing.impl.indexing.LogContext.create(LogContext.java:115) at org.netbeans.modules.parsing.impl.indexing.LogContext.create(LogContext.java:108) at org.netbeans.modules.parsing.impl.indexing.RepositoryUpdater.stateChanged(RepositoryUpdater.java:588) at org.openide.util.ChangeSupport.fireChange(ChangeSupport.java:133) at org.openide.util.ChangeSupport.fireChange(ChangeSupport.java:119)
Created attachment 128598 [details] stacktrace
Scan started by VCS changing the global visibility (marking some files as visible non visible). The source roots need to be rechecked if some files are affected by this global change.