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Hello,
All software / projects has been developed for efika1, will be compatible for efika2 out-the-box?
In theory. PowerPC software isn't like ARM or MIPS or SPARC where suddenly you change to a new processor and all your software starts running 100 times slower, or implements whole new instruction set models. It should run from an application level identically (it's the same basic processor core on the 5121E, just with some power management enhancements).
From a hardware level, it depends what features are exposed. The PPC core is the same, so that is not a problem; any kernel that booted on an Efika1 should run on an Efika2 with many features intact.
On a design with the 5200B it may be that some features are moved around (the PSC's can be configured in many ways and many other features multiplexed to get the same functionality from different configurations). These differences SHOULD be abstracted by the firmware and device tree so that Linux would not care, but if other functionality is implemented in non-abstractable ways (perhaps using a different controller for USB or audio) then some kernel work may be required to expose it for applications.
On a design with the 5121E some of the controllers are derived from the 8349E and some are brand new, so drivers will need to be written and/or exposed in Linux kernels. You may end up booting a system which has only very basic USB functionality and no SATA, no audio (PSC operation is slightly different) with a "legacy" Efika kernel. But the differences are small enough and the driver support good enough that these kernels should roll out quickly and not cause too many problems.
So, it depends what level you are looking for. You can guarantee that the Efika2 will have a 400MHz e300, stereo audio, 100Mbit/s ethernet, USB ports and an ATA disk attachment of some kind, so as long as you didn't solder anything to the board and make a custom project board in hardware that your software relies on (you would have to rework that!), that is to say as long as your project is abstracted from the PHYSICAL attributes of the Efika board, then it'll be fine.