GROMACS editor after a run: internal file names, stale status, developer text

Seen 2026-10-15 in the GROMACS MD Optimize editor after a finished minimisation (Inputs tab, read only).

Starting structure shows ecceSession_ecceMdOptimize.gro, a name built from the content type (ResourceUtils.C), instead of the attached file's name (em.gro). The editor should keep showing the name the user attached.
Status line still reads "Ready: a topology and a starting structure are attached." (GromacsInputsPanel::refresh). After a run it should say the calculation has run and its inputs are fixed until Reset.
Topology shows processed.gmxtop, the internal storage name; show processed.top, as attached.
The intro paragraph includes developer detail ("A topology is kept as .gmxtop so it cannot be mistaken for an NWChem topology; the job still sees it as topol.top."). Keep the first two sentences.

For the GROMACS round, with #334.

Cause, from the code (not yet confirmed on a run):

Structure. The attached starting structure is stored as the task's RESTART_OUTPUT file (GromacsInputsPanel: STRUCTURE = JCode::RESTART_OUTPUT), and the job stages it as conf.gro for grompp. So the run did start from em.gro. mdrun then writes its final structure as _.gro (ecceSession_ecceMdOptimize.gro, gensub ~1547), and that comes back as the task's RESTART_OUTPUT. It replaces the attached file, and the panel goes on to label the final structure "Starting structure".
- It is the right file for the next task in the study to start from, but the record of what this task started from is gone, and a Reset and rerun would start from the minimised structure, not em.gro.
Topology. processed.gmxtop is the stored copy of the attached processed.top. The rename is deliberate (so NWChem code does not take it for an NWChem topology); the content is unchanged.

Fix: keep the attached input under its own type, separate from the run's restart output. Show both:

Show the topology under its attached name.

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