[Copilot]

The "Lint, Unit Test, And Build" job failed in peptide-paired-routing.test.js (bond length 0.75 and 3). With fixedCoords supplied, generateCoords returned different coordinates for the fixed atoms. The tests expect them back unchanged.

Three cleanup paths ignored fixed atoms.

• Symmetry tidy (cleanup/symmetry-tidy.js)
  • The fused-junction snap rotated an entire component, and the axis snap moved single atoms.
  • Fixed atoms are now skipped.
  • Components containing a fixed atom are excluded from junction rotation.
• Stage runner (cleanup/stage-runner.js)
  • A stage result that moves any atom in layoutGraph.fixedCoords is no longer accepted as the best stage. This covers stages that don't check frozen atoms themselves, such as the terminal-leaf and collateral-root retouches.
  • It applies only when preserveFixed !== false.
• Large-molecule residual retouch (pipeline.js)
  • runLargeMoleculeResidualRetouch already accepts frozenAtomIds, but none of its four call sites passed it.
  • All four now pass placement.frozenAtomIds.

Review notes:

• The stage-runner check compares against layoutGraph.fixedCoords only. Atoms frozen because their component was preserved from existingCoords are not covered.
• The runner rejects a whole stage result rather than repairing it, so a stage that moved a fixed atom loses its other improvements too.