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This happens when adding a linked file !ENTRY org.eclipse.core.jobs 4 2 2011-10-07 07:05:38.937 !MESSAGE An internal error occurred during: "Re-indexing repository Prj1". !STACK 0 java.lang.NullPointerException at org.eclipse.jgit.treewalk.filter.PathFilter.create(PathFilter.java:77) at org.eclipse.jgit.treewalk.filter.PathFilterGroup.createFromStrings(PathFilterGroup.java:90) at org.eclipse.egit.core.internal.indexdiff.IndexDiffCacheEntry.calcIndexDiffData(IndexDiffCacheEntry.java:235) at org.eclipse.egit.core.internal.indexdiff.IndexDiffCacheEntry.access$6(IndexDiffCacheEntry.java:223) at org.eclipse.egit.core.internal.indexdiff.cheEIndexDiffCantry$4.run(IndexDiffCacheEntry.java:189) at org.eclipse.core.internal.jobs.Worker.run(Worker.java:54) Other problems occur when adding linked folder and if you already have linked resources delete fails. There is another bug regarding linked resources, but it predates the code that crashes here.
This issue has been fixed somewhere.