EAMxx namelist/buildnml/atmchange remaining tasks and wishlist

I am opening this issue to track stuff that still needs to be done for our handling of namelist in v1. Feel free to add items that you think are needed or simply desirable.

In the following, `def.xml` is the XML file with our defaults, while `eam.xml` is the intermediate xml file generated by buildnml.

- [x] Store the timestamp of the case XML files in `eam.xml` file. When buildnml runs, compare the current timestamp of those files with the one stored in `eam.xml` (if this file is already present). If some timestamp differ, nuke `eam.xml` and re-generate it. Bonus: store all the atmchange issued by the user in `eam.xml`, so that, if we have to re-generate it, we can re-issue them.
- [x] Currently, `atm_procs_list` for the whole atm is a "locked" entry, meaning it can be changed via `atmchange`. However, one _may_ want to swap a parametrization for another, without having to create a new compset. Or one might want to remove a parametrization, without the need to add a new compset. It might be therefore desirable to allow to modify this entry. However, modifying it, one might add an atm proc that was not there, and whose params didn't make it to `eam.xml`. Therefore, if one modifies this entry, we should re-generate the section `atmosphere_processes`, parsing `def.xml` to grab all needed defaults.
- [ ] As EAMxx grows, it is possible that some parameters don't make it into `eam.xml`, but they are still used. This is probably a bug in buildnml, but in some corner cases, it might be needed. E.g., during development, one may want to try to make a new parameter configurable for a certain parametrization. Of course, the cleanest way to do this, would be to add the parameter to `def.xml`, but maybe for initial development, it's ok to just let the param in the input files without changing the defaults file. So we may consider adding a feature to `atmchange` to _add_ entries, along the line of `atmchange --add [ns1::ns2..::nsN::]param_name=XYZ`, where `[ns1::...::nsN::]` is needed only if `param_name` does not uniquely identify the parameter in `eam.xml` (just like it is already the case in `atmchange` and `atmquery`). I'm not clear if `atmchange` should error out if the parameter already exists, or simply revert to a normal `atmchange` call in that case.
- [ ] Maybe add a `--remove` to `atmchange`, to remove some parameters. I'm not sure if this would make any difference, or, more correctly, whether it _should_. It would make a difference if the code already implements some default behavior if a parameter/parameterList is not found, in which case, removing the entry from `eam.xml` might allow to achieve that. But if that's the case, maybe we have a confusing code, where the `def.xml` is not prescribing the "default" behavior of the code.
- [ ] Allow to use atm parameters as selectors, to avoid injecting ATM vars in the CIME xml settings. That is, allow the following snippet in our xml defaults file
```
one
foo
bar
```

Edit: perhaps the 2nd point can be fixed (at least for the `atm_proc_list` part) by keeping the defaults of all atm procs in the intermediate file.