Improve handling of use_lai_streams for PLUMBER2 sites

In #2155 we had to do some hacks to handle use_lai_streams where the shell_commands appends to the user_nl_clm file. The same is true for history output in BGC (default) vs. SP cases.

This is problematic, because it will keep appending every time shell_commands is run, ordering might be important, and it's problematic to clone. More robust would be to work inside of build-namelist and/or buildnml to do this by reacting to CLM_USRDAT_NAME settings for PLUMBER2.