The sample documents and related ant tasks work for a relatively simple directory structure. They assume that your content and output directory structure will be something like: sample/ |-- basefiles |-- concepts `-- tasks However, if your ditamap refers to content in other parallel project directories, your output will have a deeper path to the same files. For instance, imagine your ditamap file is in the root of the sample directory, but it includes a reference to a topic in other such as: <topicref href="concepts/foo.xml"> <topicref href="concepts/bar.xml"/> <topicref href="../other/concepts/baz.xml"/> </topicref> Referencing content in this way will force a deeper nesting to the output directory. The directory structure of your content in the output directory would now be: sample/ |-- other | `-- concepts `-- sample |-- concepts `-- tasks Note that there are now two sample directories in the output, the main one and one that is a sibling to the other directory. The files are generated by the Open Toolkit for the sample project now wind up in the deeper nested sample directory.