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Newbie question: How do I customize the rootfs during build time?

I am new to embedded development so this may be an obvious question, but here goes.  I appreciate any advice.

I am using an am335x EVM board and SDK 05.06  to develop my project. 

The SDK provides one base and one full size roofs. However, I need to customize the rootfs and add additional custom packages.  

There are instructions in the Sitara SDK (here: http://processors.wiki.ti.com/index.php/AMSDK_File_System_Optimization/Customization), but tell me to use OPKG, but my understanding about that is I would need to run the OPKG commands from the target device (via SSH), rather than something that is done at build time.

My need is to be able to build the source for the new package and I want to have the build output installed into the root file system on my development box.