Makefile: Fix various documentation build issues

This commit slighly modifies Makefiles in order to be able to build
the documentation on Debian stretch (using sphinx 1.4.9) but also
with the latest sphinx version to date (1.7.5).

Changes notably includes:

• remove the --implicit-namespaces option for sphinx-apidoc as:
  • it is not needed
  • it is not supported on sphinx 1.4.9
  • output is not correct with sphinx 1.7.5
• use sphinx -b option instead of -M for building html doc as an exception is raised otherwise when using sphinx 1.4.9