clean up packer .json and bootstrap scripts for docker build in docker branch

[paciorek]

BCE-2016-fall.json and a few bootstrap scripts (00, 45, 55) modified in somewhat kludgey ways to get docker build to work in the docker branch.

In particular took 'sudo' out of the execute_command in the json file. Perhaps 'apt-get install sudo' prior to execution of the bootstrap script sourcing.
In addition the revised .json file copies to /tmp and /tmp not to /tmp/packages and /tmp/bootstrap.d as in the docker build /tmp/packages/packages and /tmp/bootstrap.d/bootstrap.d were getting created.

Also clean up the bootstrap scripts. If we move Miniconda to /opt, we may not need to use /home/ubuntu at all and not even have an ubuntu user on the BCE docker image.