Fix sorc/upp.fd link ordering to prevent broken symlinks

[Copilot]

Description

sorc/link_workflow.sh created symlinks to files within sorc/upp.fd before the sorc/upp.fd directory link existed (lines 151-161, 397 referenced it; line 466 created it). Script failures before line 466 left broken symlinks.

Changes:

• Moved sorc/upp.fd link creation from line 466 to line 143 (before first usage)
• Added existence checks before all upp.fd symlink operations
• Removed duplicate link creation code

Before:

# Line 151-161: Create links to files in upp.fd (doesn't exist yet)
${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/params_grib2_tbl_new" .
...
# Line 466: Finally create the upp.fd link itself
${LINK} ufs_model.fd/UFSATM/upp upp.fd

After:

# Line 143-152: Create upp.fd link first
cd "${HOMEgfs}/sorc" || exit 8
if [[ -d ufs_model.fd ]]; then
    ${LINK} ufs_model.fd/UFSATM/upp upp.fd
fi

# Line 162-179: Use it safely with existence checks
if [[ -d "${HOMEgfs}/sorc/upp.fd" ]]; then
    [[ -f "${HOMEgfs}/sorc/upp.fd/parm/params_grib2_tbl_new" ]] && \
        ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/params_grib2_tbl_new" .
fi

Verified gsi.fd and enkf.fd have no similar issues.

Type of change

• Bug fix (fixes something broken)
• New feature (adds functionality)
• Maintenance (code refactor, clean-up, new CI test, etc.)

Change characteristics

• Is this change expected to change outputs (e.g. value changes to existing outputs, new files stored in COM, files removed from COM, filename changes, additions/subtractions to archives)? NO
• Is this a breaking change (a change in existing functionality)? NO
• Does this change require a documentation update? NO
• Does this change require an update to any of the following submodules? NO

How has this been tested?

• Bash syntax validation (bash -n)
• Shellcheck analysis (zero errors)
• Manual verification of link ordering and existence checks

Checklist

• Any dependent changes have been merged and published
• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have documented my code, including function, input, and output descriptions
• My changes generate no new warnings
• New and existing tests pass with my changes
• This change is covered by an existing CI test or a new one has been added
• Any new scripts have been added to the .github/CODEOWNERS file with owners
• I have made corresponding changes to the system documentation if necessary

Original prompt

---

This section details on the original issue you should resolve

<issue_title>files linked to sorc/upp.fd before sorc/upp.fd created</issue_title>
<issue_description>### What is wrong?

sorc/link_workflow.sh creates links pointing at sorc/upp.fd before the link for sorc/upp.fd is created.

151:${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/params_grib2_tbl_new" .
152:${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/fix/nam_micro_lookup.dat" .
155:    ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/${dir}" .
161:    ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/fix/chem/${file}" .
397:${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/exec/upp.x" .
463:    if [[ -d upp.fd ]]; then
464:        rm -rf upp.fd
466:    ${LINK} ufs_model.fd/UFSATM/upp upp.fd

This is unsafe. If link_workflow.sh fails before line 466 is executed, the preceding links are invalid.

What should have happened?

All links created by sorc/link_workfow.sh should be valid links.

What machines are impacted?

All or N/A

What global-workflow hash are you using?

2596d2a

Steps to reproduce

1. clone g-w develop
2. execute sorc/build_compute.sh for all components
3. modify link_workflow.sh such that it fails before the sorc/upp.fd link is created
4. execute link_workflow.sh. It aborts at the failure point you created
5. check the link $HOMEgfs/parm/post/params_grib2_tbl_new. This will be a dead link.

Additional information

This issue was stumbled upon while testing GDASApp PR #2025.

Do you have a proposed solution?

Refactor link_workflow.sh such that the sorc/upp.fd link is created before links pointing at files in sorc/upp.fd are created.</issue_description>

<agent_instructions>Examine the script sorc/link_workflow.sh and ensure that the linking in this script of directories and files within directories are in correct order. Additionally, if possible update the script to ensure that a file or directory exists before creating the link or attempt to copy.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes files linked to sorc/upp.fd before sorc/upp.fd created #4396

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[AntonMFernando-NOAA]

lgtm.

[github-actions]

[shfmt] _{reported by reviewdog 🐶}

Suggested change

	[[ -f "${HOMEgfs}/sorc/upp.fd/parm/params_grib2_tbl_new" ]] && \
	[[ -f "${HOMEgfs}/sorc/upp.fd/parm/params_grib2_tbl_new" ]] &&

[github-actions]

[shfmt] _{reported by reviewdog 🐶}

Suggested change

	[[ -f "${HOMEgfs}/sorc/upp.fd/fix/nam_micro_lookup.dat" ]] && \
	[[ -f "${HOMEgfs}/sorc/upp.fd/fix/nam_micro_lookup.dat" ]] &&

[github-actions]

[shfmt] _{reported by reviewdog 🐶}

Suggested change

	[[ -d "${HOMEgfs}/sorc/upp.fd/parm/${dir}" ]] && \
	[[ -d "${HOMEgfs}/sorc/upp.fd/parm/${dir}" ]] &&

[github-actions]

[shfmt] _{reported by reviewdog 🐶}

Suggested change

	[[ -f "${HOMEgfs}/sorc/upp.fd/fix/chem/${file}" ]] && \
	[[ -f "${HOMEgfs}/sorc/upp.fd/fix/chem/${file}" ]] &&