DITA Open Toolkit supports two different file extensions, ".dita" and ".xml". Previous releases of DITA Open Toolkit do not support the transformation of DITA maps containing inconsistent file types, such as one DITA map containing both .dita and .xml files. Though you can create either .dita or .xml files, you cannot include both kinds of files in one DITA map. This makes file reuse difficult, because you have to change the file extensions manually make them consistent in one DITA map.
In DITA OT 1.3, you can include both .xml and .dita as the file extensions in one DITA map and transform the DITA map into your desired output without manually changing the file extensions.
If you include both .xml and .dita files in one DITA map, and specify /ditaext:.dita in Java command, the .xml files are transferred to .dita files and put in the temp directory together with the .dita files. If you specify /ditaext:.xml in Java command, all the .dita files are transferred to .xml files under the temp directory. The default process option is changing all files into .xml files.
You might use other file extensions together with .dita and .xml in one ditamap as well, such as .dit, but they are not tested in DITA OT 1.3 and thus you might take the risk of transformation failure.