doc: Document .RData handoff points in core workflow functions

[S1DDHEY]

Description

This draft PR adds documentation for .RData handoff points in core PEcAn workflow functions. It focuses on improving @returnand @details sections to clarify what objects are written to disk and how they are used by downstream steps.

This work is part 1 of my pre-GSoC prep for the modularity project.

Motivation and Context

Review Time Estimate

• Immediately
• Within one week
• When possible

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• 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.
• My name is in the list of CITATION.cff
• I agree that PEcAn Project may distribute my contribution under any or all of
  • the same license as the existing code,
  • and/or the BSD 3-clause license.
• I have updated the CHANGELOG.md.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.

[S1DDHEY]

The current CI check fails because of multiple .Rd files being out of sync, not sure why there are so many of them as I have only made changes in very few files.

[infotroph]

@S1DDHEY Looks like declaring markdown=TRUE for the whole DB package made Roxygen change something in ~every Rd file.

Adopting Markdown across all our Roxygen docs is a worthy but low-priority goal, so if you're up for reviewing all the changes and confirming the changes are desirable / editing as needed, go for it.

If you'd rather not take that on in this PR, you can take markdown = TRUE out of DESCRIPTION and instead opt in the pages you edited by including #' @md somewhere in each Roxygen block that you want interpreted as Markdown.

[S1DDHEY]

@infotroph Thank you for the clarification, for this PR I'd just revert the DESCRIPTION file changes and will proceed by adding the @md tag for all the changes I did.

[S1DDHEY]

@mdietze let me know if any changes are needed for this one, I'll add the .Rd files accordingly.

[mdietze]

For errors in Rd files, make sure to fix the Roxygen, not the Rd files themselves

 checking Rd cross-references ... WARNING
  Missing link or links in Rd file 'get.parameter.samples.Rd':
    ‘run.meta.analysis.pft’ ‘run.write.configs’
  
  Missing link or links in Rd file 'get.results.Rd':
    ‘run.write.configs’
  
  Missing link or links in Rd file 'run.sensitivity.analysis.Rd':
    ‘run.write.configs’
  
  See section 'Cross-references' in the 'Writing R Extensions' manual.
  checking Rd files ... NOTE
  checkRd: (-1) get.parameter.samples.Rd:36-44: Lost braces
      36 | \\describe{
         |           ^
  checkRd: (-1) get.parameter.samples.Rd:37: Lost braces
      37 | \\item{\code{post.distns.Rdata} or \code{prior.distns.Rdata}}{Posterior (or prior)
         |       ^
  checkRd: (-1) get.parameter.samples.Rd:37-39: Lost braces
      37 | \\item{\code{post.distns.Rdata} or \code{prior.distns.Rdata}}{Posterior (or prior)
         |                                                              ^
  checkRd: (-1) get.parameter.samples.Rd:40: Lost braces
      40 | \\item{\code{trait.mcmc.Rdata}}{(Optional) MCMC chain samples from the
         |       ^
  checkRd: (-1) get.parameter.samples.Rd:40-43: Lost braces
      40 | \\item{\code{trait.mcmc.Rdata}}{(Optional) MCMC chain samples from the
         |                                ^
  checkRd: (-1) get.parameter.samples.Rd:47-61: Lost braces
      47 | \\describe{
         |           ^
  checkRd: (-1) get.parameter.samples.Rd:48: Lost braces
      48 | \\item{\code{samples.Rdata}}{When \code{save_to_disk = TRUE}, bundles 5 objects:
         |       ^
  checkRd: (-1) get.parameter.samples.Rd:48-60: Lost braces
      48 | \\item{\code{samples.Rdata}}{When \code{save_to_disk = TRUE}, bundles 5 objects:
         |                             ^
  Error: Please fix these and resubmit.

[S1DDHEY]

@mdietze All required CI checks are passing now, had a few typos.