Change `model2netcdf.ED2()` to include more variables from monthly -E- files and group by PFT

[Aariq]

Mainly tackling https://github.com/PecanProject/pecan/issues/2997. Likely fixing other issues and changing some behaviors along the way.

Description

• renamed and deprecated begins, ends, and out args in put_E_values() and put_T_values()
• Read in additional ED2 output variables in read_E_files()
• Behavior of read_E_files() changed somewhat significantly: previously, variables were weighted by plant density in each cohort. This weighting has been removed. Instead, any variables in per-plant units are now converted to per area units using plant density.
• add unit conversions to PEcAn standard
• fix bug/incorrect documentation of out argument in put_E_values()
• Revert changes to the pft argument for model2netcdf.ED2() and the read_*_files() functions to be a named numeric vector instead of the settings$pfts list. If settings is supplied, new helper function extract_pfts(settings) will return a named vector.
• Document functions
• changed message about failed runs from "info" to "warning" (indicates problems since ensemble runs may not be failing at random)
• changed put_E_values() and put_T_values() to unexported.
• Added tests

Motivation and Context

Only a small number of variables were being read from monthly E files and put into the .nc files output by model2netcdf.ED() and they were not being converted to PEcAn standard. This PR adds more variables to that list and hopefully establishes some generalizable patterns for adding more variables in the future.

Closes #2997

Review Time Estimate

• [ ] Immediately
• [ ] Within one week
• [ ] When possible

Types of changes

• [ ] Bug fix (non-breaking change which fixes an issue)
• [x] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• [ ] My change requires a change to the documentation.
• [x] My name is in the list of CITATION.cff
• [ ] I have updated the CHANGELOG.md.
• [x] I have updated the documentation accordingly.
• [x] I have read the CONTRIBUTING document.
• [x] I have added tests to cover my changes.
• [ ] All new and existing tests passed.

[Aariq]

Just for the record, I think it's pretty hard to work on this group of functions because read_*_files() does some conversions and put_*_values() does additional conversions and adds the units. I think it would be a lot simpler and easier to work on if the "read" and "put" steps were combined, but that would be a much bigger re-write than I'm already doing.

[Aariq]

Ok, all tests are passing (not check() though). I think the only thing left is to name the pft-level variables pulled from the monthly E files something standard and then deal with devtools::check() issues.