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If you name your template "X" and in the generated wizard choose "/tmp" as the location (so that it shows "/tmp/X" as the project location), the project is actually created in /tmp/X/X. The line dir = dir.createFolder(name); looks to be responsible. Try deleting it.
Should be fixed now. committed Up-To-Date 1.5 apisupport/project/src/org/netbeans/modules/apisupport/project/ui/wizard/project/templateWizardIterator.javx
verified