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JDevil is a java dependency visualization library. It analyses and visualizes dependencies between java classes, packages and libraries. Generation of raster images or SVG is possible via Java API or Ant plugin.
The Docbook Plugin for Eclipse will allow generating documents within Eclipse IDE environment to various file formats that docbook supports using docbook xsl. Possible future enhancements could include support for docbook dsssl and apache's FOP support.
JTourBus is an Eclipse plugin for navigating source code based on the idea of tours. Tours can be created using JavaDoc-tags (technically annotations work as well) supported by a little UI.
Jdeluxe is an Eclipse Plugin that helps developers to analyse B2B interfaces based on XML Standards. It is designed to be highly adaptable and uses generic XQuery-calls to extract documentation data. Data can be stored in a Web Repository via Web Service
BibTeXlipse is an Eclipse plugin for managing and analyse bibliography databases. Mainly for BibTeX databases, but will import and export many other bibliographic formats.
It's currently in planning phase.