Keep every column of probe output in golden packs

[sbryngelson]

Fixes #1711.

The defect

toolchain/mfc/packer/pack.py treats every .dat file under D/ as a spatial field of the form <x> [<y> <z>] <value>, infers dimensionality from the first line, and keeps only the last column of each row:

ndims   = len(_extract_doubles(content.split("\n", 1)[0])) - 1
doubles = _extract_doubles(content)[ndims :: ndims + 1]

Probe output is not a spatial field. It is a multi-column time series whose columns are distinct physical quantities, and the set varies by configuration:

Configuration	Columns written
1D, general (m_data_output.fpp:1519)	nondim_time, rho, vel(1), pres
bubbles (line 1490)	nondim_time, rho, vel(1), pres, alf, R, Rdot, nR, nRdot
hypoelastic (line 1515)	nondim_time, rho, vel(1), vel(2), pres, tau_e(1..3)
3D (line 1524)	nondim_time, rho, vel(1..3), pres, gamma, pi_inf, qv, c, accel

Under the field interpretation only the final column survived. In 3D that means the golden validated the acceleration magnitude and discarded density, velocity, pressure, gamma, pi_inf, qv, and the sound speed.

lag_bubble files were already special-cased for exactly this reason. Probe files are the remaining case.

Change

Retain every column for probe files. No header line to skip — s_write_probe_files writes data rows only.

Effect on existing goldens

Golden	Before	After
tests/5CAA4E68 (1D exp_bubscreen)	50 values	450
tests/FBB296DA (1D bubblescreen)	50 values	450
tests/AE9A7D73 (1D poly_bubscreen)	1 value	9

Nine columns per row instead of one. The added values are what was being dropped: density, velocity, pressure, void fraction, and the bubble radius/velocity moments. That widening is the point of the change — it is coverage these cases should always have had.

The regenerated metadata records (dirty). That is inherent to regenerating tracked goldens: writing them dirties the tree before the metadata is stamped. Newly added goldens do not have this problem.

Verification

The three probe cases pass against their regenerated goldens. The change is gated on "probe" in short_filepath, so non-probe files take the original code path unchanged and no other golden should move. A full local suite run confirms it: 627 passed, 0 failed.

An earlier run of the same suite reported the three probe cases failing with "Variable count didn't match". That did not reproduce — the three pass in isolation, pass on consecutive repeat runs, and pass in the clean full-suite run above. It matches non-reproducible flakiness seen on an unrelated branch this session (two chemistry cases, likewise green individually), and appears to be local contention at high -j rather than anything in this change. Worth knowing it has been seen, in case CI shows it.

Why now

#1707 is a defect in the probe sound speed. It could not be given a regression test through the normal golden path, because c is never the last column in any configuration — a case could exercise the defective code, emit visibly wrong output, and still pass. This PR is a prerequisite for testing that fix, and stands on its own regardless.

Note that even with this change, observing c specifically requires a 3D probe case; the 1D writes do not emit it at all.

[Copilot]

Pull request overview

This PR updates the golden packer so probe .dat outputs under D/ are treated as multi-column time series (retaining all columns) instead of being misinterpreted as spatial fields (which previously retained only the last column). This improves regression coverage for probe diagnostics that are not in the final column.

Changes:

• Special-case probe outputs in toolchain/mfc/packer/pack.py to retain all numeric columns.
• Regenerate affected probe-based golden packs to include the full probe column set.
• Update golden metadata files produced during regeneration.

Reviewed changes

Copilot reviewed 6 out of 7 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
toolchain/mfc/packer/pack.py	Adds probe-specific parsing path to retain all columns for probe outputs.
tests/FBB296DA/golden.txt	Updated golden pack content reflecting full probe columns.
tests/FBB296DA/golden-metadata.txt	Updated provenance metadata for regenerated golden.
tests/AE9A7D73/golden.txt	Updated golden pack content reflecting full probe columns.
tests/AE9A7D73/golden-metadata.txt	Updated provenance metadata for regenerated golden.
tests/5CAA4E68/golden-metadata.txt	Updated provenance metadata for regenerated golden.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 60.77%. Comparing base (8dfe8c7) to head (c185dc8).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1712   +/-   ##
=======================================
  Coverage   60.77%   60.77%           
=======================================
  Files          83       83           
  Lines       20872    20872           
  Branches     3101     3101           
=======================================
  Hits        12685    12685           
  Misses       6121     6121           
  Partials     2066     2066           

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