manual: Clarify wrapper and debug

Try to clarify how the wrapper passes arguments and why.
This is mainly because the output you can see when you build, does not
reflect what is invoked by the wrapper.

Signed-off-by: Maxime Hadjinlian <maxime.hadjinlian@gmail.com>
Signed-off-by: Peter Korsgaard <peter@korsgaard.com>