This is for setting up Cocoon on JRun. Specifically, I am using JRun on NT.

1. Move parser/IBMXMLParser.java and /parser/SunXMLParser.java to a new
   directory parser/not_used
2. Move processor/LotusXSLProcessor.java to a new directory processor/not_used
3. If you are using a JRun that can't set init args when triggering a servlet
   based on filename, then you must modify line 94 of Cocoon.java to:
   configurations = ConfigurationFactory.getConfiguration
     ("/cocoon/bin/cocoon.properties", INTERNAL_PROPERTIES);
   (or wherever your properties file is)
4. Modify line 179 of Cocoon.java from:
   String basename = request.getPathTranslated();
   -to-
   String basename = "c:/myxmldir/"+request.getRequestURI();
5. Run the 'make' batch file to recompile cocoon. If you don't already have this
   in your class file, modify make.bat to the following:   

javac -classpath \cocoon\bin\xslp.jar;\cocoon\bin\openxml.jar;\jrun\lib\jrun.jar;\jrun\lib\servlet.jar -d .\temp .\org\apache\cocoon\*.java .\org\apache\cocoon\parser\*.java .\org\apache\cocoon\processor\*.java .\org\apache\cocoon\printer\*.java .\org\apache\cocoon\framework\*.java .\org\apache\cocoon\cache\*.java

6.  You will also need to set JRun to process any request for a *.xml file 
    using "org.apache.cocoon.Cocoon". Do this per JRun instructions.

To skip the manual code adjustment with item #3, do the following:

Associate *.xml files with alias 'xml'
Create an alias xml to go to org.apache.cocoon.Cocoon
Add init arguements as needed. You at least need:
properties=/cocoon/cocoon.properties