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There is no obvious reason for having two different SPEC variables, definitions, and pathes for the Pandaboard platform. It even lead to problems regarding the omap4 framebuffer driver (look at issue #505 and #506).
This is generic part of the Genode implementation. It consists of two parts: :_Core_: is the ultimate root of the Genode application tree and provides abstractions for the lowest-level hardware resources such as RAM, ROM, CPU, and generic device access. All generic parts of Core can be found here - for system-specific implementations refer to the appropriate 'base-<system>' directory. :_Base libraries and protocols_: that are used by each Genode component to interact with other components. This is the glue that holds everything together.