Here are some best practices for organizing files and folders in DITA. Make sure maps are at the root level, and everything else exists as files or folders below the map.
When you're organizing your DITA files, it may be unclear about the right structure to use. Although you can use a variety of methods to organize your files, note the following limitations:
  • The DITA Map file might have trouble loading topics in higher level folders. DITA Map files are like kings. They want all the other files to sit below them either in the same folder or in subfolders. Oxygen has a special parameter override you can set if you're referencing topics in higher folders than the map.
  • References to a file will be more likely to break if you use subfolders. For example, suppose you put all your configuration topics into a folder called "configuration". References to a topic there will look like this: configuration/sample_config.dita. Suppose you decide to move sample_config.dita into another folder. All your links will break. (To change folder paths, I believe you use the refactoring options, but honestly I haven't quite figured them out.)
  • I do put images and glossary items in their own subfolders.
  • I always name my ditamap docmap.ditamap.

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