[rogeriojorge]

Stacked on #62. Review #62 first.

Problem

plot assumed exactly two species, a 1D run along y, and input keys (dn1, nx, k_norm) that only the default two-stream case defines. It failed or showed the wrong panels for any other case, so every example carried its own plotting code.

Change

plot(output, save=None, show=True) now works for any number of species and any dimension, in the spirit of JAX-in-Cell's single automatic figure. It draws these panels:

Panel	Content
Energy exchange	Electric and magnetic field energy, and the change in kinetic energy of each species
Energy conservation	|W(t)/W(0) − 1|
Strongest modes	The four strongest electric-field modes, labelled by their wavevector
Hermite spectrum	Per species: Σ_k |δC_n|² against Hermite order and time, which shows phase mixing, recurrence and the reach of the closure
Phase space	Per species: the perturbation f − ⟨f⟩_x at the last saved time, along the longest direction
Field map	In 2D or 3D only: the strongest field component in the plane

Other changes:

• phase_space(output, species, time_index) is exposed for custom figures.
• diagnostics also returns electric_energy and magnetic_energy.
• Command line: spectrax input.toml runs the case, saves input.png next to the file, and shows it. --no-show is for batch runs.

_plot.py shrinks from 127 to 121 lines while covering every case.

Tests

• The CLI runs a three-species 2D TOML and writes the figure.
• The full suite passes, 11 tests in 9 s.
• The figure was checked visually on Landau damping and on a 2D two-species case.