Tonight I just finished creating a JSON index file for the Boards Manager that is compatible with both the Arduino and Energia IDEs. I've successfully tested compilation and flashing through both IDEs. For some reason the current JSON index file was only compatible with Energia, and would cause Arduino IDE to throw java null pointer exceptions. After reworking the file it's properly parsed by both IDEs.

Something learned along the way:

When building a custom JSON index file for theBoards Manager, toolsDependencies.packager should match the top level packages.name value where the tools are described.

For instance when building the new file I had to make in order to have arm-none-eabi-gcc compiler and dslite flasher installed along with this board.

packages.platforms.toolsDependencies.packager = packages.name