added makefiles to service and software commands

To make the command developing workflow more convenient added Makefiles
making some tasks easy to do.
build improvements and fixes

Fixed a bug, where the making of README.txt failed when running setup.py
from another directory.
documentation of commands included in the main one

Commands documentaion can be built as a part of the main documentation.
All that is needed is to export INCLUDE_COMMANDS=1 before running
`make html`.