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Best Practice for Handling Bootloader and Main Application in Embedded Studio

I'm currently working on an application for Nordic that contains a bootloader and a main application using Embedded Studio.  Most of the development will be on the main application as the bootloader is fairly basic.  Right now, when we need to load a new main application on the firmware, we need to regenerate the bootloader settings page and merge everything together manually.  Is there a way in embedded studio to automate this process during either a load or build?  I couldn't find any post-build command sections in the project settings to help automate this.  Am I just missing a simple setting?  How do others handle this situation?

EDIT: Right after posting I found the Pre and Post Build commands.  However, I'm still interested to hear how others are handling it.

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