After installing the Java CS SDK refer to the README.txt file in the jcs-sdk-home directory. The file explains how the ANT build harness works, and information about a preconfigured project and launcher for the Eclipse IDE. Typically the best approach for debugging is to use Eclipse, or your alternative IDE.
However, to debug remotely, there are some flags you are required to provide on the "java" command-line used to run the Java CS. You can refer to these flags in the jcs-sdk-home/bin/jcs.bat file which can be used as an alternative way to invoke a development Java CS (rather than using your IDE). The flags are "-Xdebug -Xrunjdwp:server=y,transport=dt_socket,address=8787,suspend=n".
Note: For more information, see http://www.ibm.com/developerworks/opensource/library/os-eclipse-javadebug/index.html which is a useful reference article.
Be aware of the following:
LOCAL_MACHINE\SOFTWARE\ComputerAssociates\Identity Manager\Procrun 2.0\im_jcs\Parameters\Java
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