Help building patched android framework

Question

I am new to Android platform development. I have just succeded building Cyanogenmod 7 sources after applying a patch, which adds extra jars to the system (fit into /system/framework directory).

After flashing the device and checking that the new custom jars are there, and decompiling (extracting classes.dex and running dex2jar) just to verify that the needed classes are there, I see my test program crashing due to ClassNotFound exceptions.

Since the compiled custom java sources seem ok, have I missed something in the building process so my applications can use these new framework classes?

UPDATE:

I realized that framework jars are included inside an environment variable called BOOTCLASSPATH, which is defined in init.rc. I modified it to include the new jars from SEEK project (smartcardapi.jar and org.simalliance.openmobileapi.jar). I rebuilt the image and flashed my phone.

The device now does not start. I have read something here about class optimizations that are run against BOOTCLASSPATH classes. The advice is not to mess with BOOTCLASSPATH.

But what can I do so my applications can use the extended API classes defined in the new jars?