deploy tool project classpath

Our application reads configuration information from two external Java properties files. One of these files must be located in the classpath. Since the application was not developed in NWDS (we use Eclipse 3.x), we use the deploy tool to deploy the EAR (containing WAR and EJB jar). We tried using the project classpath in the project options of the deploy tool to specify the local directory where to find the Java properties file. However, this did not work as our app was unable to find the file. We had to put the directory on the JVM's system classpath, which is not ideal.

How exactly do the entries specified for project classpath get inserted into the class loader heirarchy of NetWeaver AS? Or do they? I have read "Extended Java Class Loading of SAP NetWeaver" but did not see any mention of the project classpath set using the deploy tool.