Issues after DBEN merge

[stineb]

@lauramarques

Remaining issues after merge:

• I corrected some erroneous annual cohorts output writing. But some remain. See compilation warnings. Please resolve them.
• Update documentation of biomee R functions with revised output variables

Please take note of the following changes I had to make on the master branch after your PR was merged:

• output_annual_cohorts_nsn written multiple times in SR biomee_f. I corrected it now.
• I changed timings and frequency of output writing output_annual_cohorts to how it was before
• I commented out "Reset vegetation to initial conditions" in SR biosphere_annual
• I removed validation plant C line in biomee_use vignette

[lauramarques]

About the issues after merge:

• I do not see any warning when compiling. Not sure what you mean here.
• Can you please point me to the file for updating the documentation of biomee R functions?

About the changes:

• I cannot find the duplicated output_annual_cohorts_nsn but if it is corrected now, fine.
• OK. I changed it to test the different cohort outputs, but I guess we can keep it to get the outputs after the spin-up years.
• I think we can keep the reset_vegn_initial as it runs when do_reset_veg = TRUE in params_siml.
• OK, that is fine.

[stineb]

• The documentation is in the header of the R function file run_biomee_f_bysite().
• I get warnings like this one here:

sofun_r.f90:342:37:

  342 |     output_annual_cohorts_c_deadtrees,  &
      |                                     1
Warning: Dummy argument 'output_annual_cohorts_c_deadtrees' at (1) was declared INTENT(OUT) but was not set [-Wunused-dummy-argument]

• We should avoid (or keep to an absolute minimum) output writing during spinup. Otherwise, the returned output objects are too large.
• "I think we can keep the reset_vegn_initial as it runs when do_reset_veg = TRUE in params_siml." That's fine as a temporary fix, but should eventually be replaced by reading the disturbance (equivalent to harvesting) from the forcing time series. I have implemented this in branch disturb.