I am currently working on a large PHP CMS / Framework and documenting it extensively as I go along. In addition to phpdoc-style inline comments, I need to document XML structures, details on concepts and practices, write HOWTOs and so on.

At the moment, I am using simple OpenOffice documents for that, but I'm unhappy with it and looking for a "real" documentation system.

So, I am looking for recommendations for robust, minimalistic, easy-to-use documentation software.

I have tried a number of Wikis, most prominently Dokuwiki. I like the open-minded approach, the freedom in editing, and the simplicity, but they provide little support in structuring a multi-chapter documentation, and make basic reorganisation tasks very difficult (e.g. moving pages to a different namespace). Working with the plugins is Cumbersome, and they are not really easy to use.

Open Source would be a plus but is not a requirement.

Thanks for all the suggestions. I have not had time to look into each one in detail. I will be trying Sphinx, especially because it provides so much support for a good structure. I may update this post later when I'm done and report how it worked out.

The suggestions

Trac's built-in wiki which is great but for my taste provides too little support for keeping a structure - it's perfect though for "normal", smaller size project documentation

Markdown my current favourite because of its minimalism, however not sure yet whether maintaining a structure will be easy enough. A Markdown-Based system would of course be very easy to extend, e.g. to look up cross references from the project's code base. Of course it would be great to find something that already has that out of the box.

The DocBook format and to edit, the commercial Oxygen XML Editor - a great standard for building documentation, no doubt. Maybe too "technical" for my purposes as I need something to open quickly, write into and go on coding. Still always worth a mention.

Sphinx an Open Source, Python based documentation generator, promising structured documentation and extensive cross-referencing. Interesting and will take a look.

Confluence a commercial but very affordable Wiki.

XWiki, an Open Source playing in Confluence's league with numerous extensions and connectors to Eclipse and Microsoft Office.

TiddlyWiki an open-source Wiki.