Avoid errors due to host Lmod in containers

These changes ensure that environment variables that are automatically passed
to the container don't interfere with Lmod inside of the container. The previous
implementation would not take care of sticky packages from the outside and Lmod
would try to reload them.

Note that Lmod defines the 'module' bash function, which doesn't propagate to
the final shell when using 'singularity shell'. If the 'module' command is needed
a login shell needs to be launched:

$ singularity exec <CONTAINER> bash -l