Issues

• memory_confirm matches entry_name by substring and promotes the first staging file that contains it

  HolobiomicsLab/Magnolia-AI#22 · Filter by author matthewhirschey opened on Oct 22, 2026

• compchem-memory prints [boot-timing] lines to stdout, corrupting the stdio MCP channel

  HolobiomicsLab/Magnolia-AI#21 · Filter by author matthewhirschey opened on Oct 22, 2026

• Session journal records a tool that returned success: false as tool_success

  HolobiomicsLab/Magnolia-AI#20 · Filter by author matthewhirschey opened on Oct 22, 2026

• xtb_optimize does not report the optimised geometry when the input is not XYZ

  HolobiomicsLab/Magnolia-AI#19 · Filter by author matthewhirschey opened on Oct 22, 2026

• gromacs_parse returns no energy terms for any .edr file

  HolobiomicsLab/Magnolia-AI#18 · Filter by author matthewhirschey opened on Oct 22, 2026

• gromacs_setup never completes: the generated ions.mdp sets an integrator GROMACS rejects

  HolobiomicsLab/Magnolia-AI#17 · Filter by author matthewhirschey opened on Oct 22, 2026

• No reproducible evidence bundle: the memory corpus behind reported results is gitignored

  enhancement
  HolobiomicsLab/Magnolia-AI#9 · Filter by author lfnothias opened on Sep 3, 2026