Drop including "yade/" folder in cpp and hpp files.

Many years we had a symlink in build-dir "yade" which
points to a source dir. It was neccessary for scons build
system, which is not the case at the moment. All headers
must be included directly without "yade/" prefix, e.g.:

<core/Scene.hpp>
<pkg/common/Sphere.hpp>
Fix docs-generation.

Revert the previous behaviour, calling sphinx.main function.
It seems, new versions of sphinx are calling sys.exit() after
execution, which breaks our doc generation.

Now SystemExit is catched by try-except block.