Container commands

[JoshuaWatt]

Reworks the way that commands specified by the user are wrapped by Pyrex. Instead of completely replacing the container commands, the user commands override and extend the container command defintions, taking precedence over them (i.e. if the user excludes a command it will be excluded even if the container includes it, and if the user includes it, it will be included even if the container excludes it).

In order for this to work, the user command shims must be individually written to execute the full path to the command inside the container, since we don't know if it will be in $PATH.

[JoshuaWatt]

This is PR #51 moved to it's own branch