build: simplify headers management and remove recursion

There is no real reason to keep the include directory a multi-level
recursion, so instead declare everything within include (so that we
can use proper nobase_ declarations) and be it.

Please note that since we removed the sub-Makefile.am, ./configure
will not create the directory structure for us on out-of-tree builds,
so we have to make sure the directory we're generating to exists first.

Signed-off-by: Diego Elio Pettenò <flameeyes@flameeyes.eu>

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