Improve new build system

Description

As Xavier pointed out, the new Makefile.am in src/ did not handle include files properly. This is fixed now. Moreover, there is now the option to call make NODEP=1 which will ignore the dependencies due to the modules and only recompile the files that are changed, taking into account include files.

Fixes #119 (closed)

News snippet

Improve new build system (dependencies of include files, possibility to ignore module dependencies)

Checklist

• I have checked that my code follows the Octopus coding standards