Refactor update command
Add version check to run command

As per: https://github.com/subuser-security/subuser/issues/127
Don't categorize programs without a set last-update-time as being out of date
Import subuserlib.update in run.py
Use a static dns server for now, untill the docker folks deal with their various dns issues.
Add multiple repository support and config file support

Fixes https://github.com/subuser-security/subuser/issues/11
Fixes https://github.com/subuser-security/subuser/issues/12
Rename getInstalledDependencies to getInstalledDependents

Fixes https://github.com/subuser-security/subuser/issues/128
The setting bin was renamed to bin-dir
Fix arguments for installProgramFromDockerfile
Fix, moved some functions to another module and didn't update their references
reference shadowing error
Change order of update command so it asks you if you want to cintinue before it continues
Reference error in update command
permissions path is now returned as None when it doesn't exist.
Show an error if repositories.json is invalid JSON.
Rename installCommon to install
Document the installed-programs.json file format.
Rename programNewRegistry to newProgramRegistry
Clean up CHANGELOG.md
Run apt-get update before installing vim