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When configuring the Eclipse IDE (http://www.eclipse.org/) for development in Java using the MapGuide Open source web API here are some useful configurations :
1) Set the environment variable : MENTOR_DICTIONARY_PATH to the (MG install dir)/share/gis/coordsys directory
2) Set the native library path to (MG install dir)/webserverextensions/lib/
3) Include the current jar : MapGuideApi*.jar in the java build path (jar can be located in $(MG install dir)/webserverextensions/www/WEB-INF/lib/
The above is the configuration for the 'Indigo' release of Eclipse but should be applicable to any current release.
(Thanks to EB for some of the input)