Yes: don't worry. That's Unix.
> a small example is a smallish ext2 / filesystem
> and the rest being a fat filesystem to that
> it can be accessed from both windows and linux.
> and there is not enough space on the ext2 to compile a kernel anymore.
There's a very simple means to "solve" that scenario, if you are the
one in a million people who happens to have such a setup, _and_ want
to recompile your kernel from scratch: create a loop mount file on the
FAT partition, create an ext2fs there, mount that, and compile on it.
Problem solved.
best regards
Patrick
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