Remove hardcoded assumption that model output lives in outdir/out

[Akash-paluvai]

Description

This PR removes hardcoded assumptions in workflow modules that model output
always lives in file.path(settings$outdir, "out"). The affected modules now
consistently use settings$modeloutdir, which respects user-defined output
locations provided via XML configuration.

A repository-wide search was performed to ensure no additional workflow
code relied on this assumption.

Motivation and Context

PEcAn already supports a configurable <modeloutdir> setting that defaults to
file.path(outdir, "out") when not explicitly provided. However, some workflow
modules were still hardcoding outdir/"out", causing user-specified
<modeloutdir> values to be ignored.

This change aligns workflow code with existing settings logic and documented
behavior, ensuring consistent handling of model output directories.

Fixes #3439

Review Time Estimate

• When possible

Types of changes

• Bug fix (non-breaking change which fixes an issue) — Fixes Remove assumption that $modeloutdir == $outdir / "out" #3439
• 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.