What function(s) should write config files to `settings$host$rundir`?

[Aariq]

Bug Description

runModule.run.write.configs(settings) appears to attempt to copy the files in settings$outdir/run/ to settings$host$rundir. This is currently failing for me (not sure why), but it doesn't seem to matter because runModule_start_model_runs() also copies config files to settings$host$rundir.

To Reproduce

My pecan.xml:

<?xml version="1.0"?>
<pecan>
  <info>
    <notes>Park Falls WLEF</notes>
  </info>
  <outdir>/data/output/pecan_runs/transect_runs/ed2_transect_WL</outdir>
  <database>
    <bety>
      <driver>PostgreSQL</driver>
      <user>bety</user>
      <password>bety</password>
      <host>postgres</host>
      <dbname>bety</dbname>
      <write>FALSE</write>
    </bety>
    <dbfiles>/data/dbfiles</dbfiles>
  </database>
  <pfts>
    <pft>
      <name>SetariaWT</name>
      <ed2_pft_number>1</ed2_pft_number>
    </pft>
    <pft>
      <name>temperate.Northern_Pine</name>
      <ed2_pft_number>6</ed2_pft_number>
    </pft>
    <pft>
      <name>temperate.Early_Hardwood</name>
      <ed2_pft_number>9</ed2_pft_number>
    </pft>
    <pft>
      <name>temperate.North_Mid_Hardwood</name>
      <ed2_pft_number>10</ed2_pft_number>
    </pft>
    <pft>
      <name>temperate.Late_Hardwood</name>
      <ed2_pft_number>11</ed2_pft_number>
    </pft>
  </pfts>

  <meta.analysis>
    <iter>300</iter>
    <random.effects>TRUE</random.effects>
    <threshold>1.2</threshold>
    <update>FALSE</update>
  </meta.analysis>
  
  <ensemble>
    <size>50</size>
    <variable>NPP</variable>
    <samplingspace>
      <parameters>
        <method>lhc</method>
      </parameters>
  </samplingspace>
  </ensemble>

  <model>
    <type>ED2</type>
    <binary>/groups/dlebauer/ed2_results/global_inputs/ed2_2.2.0_singularity.sh</binary>
    <id>14</id>
    <edin>/pecan/models/ed/inst/ED2IN.r2.2.0</edin>
    <config.header>
      <radiation>
        <lai_min>0.01</lai_min>
      </radiation>
      <ed_misc>
        <output_month>12</output_month>
      </ed_misc>
    </config.header>
    <phenol.scheme>0</phenol.scheme>
    <ed2in_tags>
      <PFT_1ST_CHECK>0</PFT_1ST_CHECK>
      <IED_INIT_MODE>0</IED_INIT_MODE>
      <MAXCOHORT>0</MAXCOHORT>
      <MAXPATCH>0</MAXPATCH>
    </ed2in_tags>
  </model>

  <run>
    <site>
      <id>678</id>
      <met.start>2019-01-01 00:00:00</met.start>
      <met.end>2019-12-31 23:59:59</met.end>
    </site>

    <inputs>
      <met>/data/sites/MERRA_ED2_site_0-678/ED_MET_DRIVER_HEADER</met>
      <veg>/data/oge2OLD/OGE2_</veg>
      <soil>/data/faoOLD/FAO_</soil>
      <lu>/data/ed_inputs/glu/</lu>
      <thsum>/data/ed_inputs/</thsum>
    </inputs>

    <start.date>2019-01-01</start.date>
    <end.date>2019-12-31</end.date>
  </run>
  
  <host>
      <name>puma</name>
      <folder>/groups/dlebauer/ed2_results/pecan_remote</folder>
      <qsub>sbatch --job-name=@NAME@ --account=dlebauer --ntasks=28 --nodes=3 --time=25:00:00 -o @STDOUT@ -e @STDERR@</qsub>
      <qsub.jobid>.* ([0-9]+)</qsub.jobid>
      <qstat>'squeue --job @JOBID@ &amp;> /dev/null || echo DONE'</qstat>
      <prerun>module load openmpi3</prerun>
      <modellauncher>
        <binary>/groups/dlebauer/ed2_results/pecan/contrib/modellauncher/modellauncher</binary>
        <qsub.extra>--partition=standard</qsub.extra>
        <mpirun>module load openmpi3; mpirun</mpirun>
      </modellauncher>
  </host>

</pecan>

Expected behavior

It's not clear from the documentation which function is supposed to be doing this, but I'd think only one of them should. My vote is for the one that currently works for me 😆.