update doc to explain how to checkout private git repository
minor doc update
use the generic run.sh command as the container CMD

run.sh will try to run a script (path to this script should be given in the
BEFORE_RUN_SCRIPT env variable) before exec the actual command (which should be
given in the EXEC_CMD env variable).
add the run.sh file to the container image
s/RUN/EXEC/
make GIT_REPO_PATH and GIT_WORKDIR_PATH envs visible in the Dockerfile