So you think the Navy (and their contractors) will be maintaining their own fork of linux and continually port changes over from mainline linux into their fork? I doubt they are that ambitious/stupid. It'll be much much easier for them to get whatever changes they make accepted into the mainline and maintained as 1st class pieces of the kernel.
I expect them to "maintain their own fork of Linux" in exactly the same way they "maintained their own fork of Windows". It seems very likely they're just porting over pure userspace-stuff. If Windows worked for them at all I doubt kernel-space stuff is necessary.
