Short term goals (v1.x)

add a "Colors" menu to the image viewer to adjust color settings for the current image (unlike the defaults in the perferences) including assigning colors to individual atom types.
Support color by property (e.g. scan computes or fixes with per-atom data), define colormaps etc.
Add a "Diameters" dialog where diamaters can by specified by atom type
implement data file manager GUI with the following features:
- import coordinates and topology via VMD molfile plugins
- import coordinates and topology from intermol
- import coordinates and topology from OpenBabel
- store data internally in a generalized YAML format
- add/remove columns to per-atom data
- change atom style for export to data file
- merge one system to another
- edit mapping between numeric and symbolic types. create labelmaps.
- import/export LAMMPS data and molecule files
- store coordinates internally as unwrapped coordinates
- recenter coordinates
- edit box boundaries
- readjust box to extent of atoms (with or without estimated radius)
- call to LAMMPS to create geometries from lattices (with/without molecule files) and STL files
- call to LAMMPS to generate visualizations of geometries
- edit force field parameters, e.g. apply charmm
- edit / manage labelmap

Long term ideas (v2.x)

rewrite entire application to build the App and its layout manually
also a rewrite should establish consistent naming conventions. now we have a mix of LAMMPS style, Qt style, and others.
add option to attach a debugger to the running program (highly non-portable, need customization support in preferences)
write a "wizard" dialog that can be used for beginners to create an input file template for a few typical use scenarios (could perhaps use some LLM based KI to look up suggestions for answers?).