docs: note dependencies for PDF generation

Probably lots of dependencies missing, these are what I needed _after_
getting regular html docs working.
[BUILD] Fix the correct make behavior if compiling inside tree

On linux, the output of CP rule was try to write to / which is - of course, forbidden for write.

This solution adds to each part of lib correct pointer to the root of lib where the libs should be written.

Bug found by Kuldeep Singh Dhaka.
cm3/common.h: Cast addr in BBIO_xx() macros. BBIO_xx has 4 byte size.
stm32: dac: buffer enable bits were inverted.
include/libopencm3/cm3/common.h: Fix CRLF.
[FIX] Fix the ATOMIC suport.