[META] Refactor opportunities

[waltsims]

Umbrella issue rolling up the standing refactor backlog. The individual issues below are scoped, low-risk cleanups that don't block any user but are worth picking up when touching the surrounding code.

Bundled here

• Refactor package file layout #219 — Promote kWaveArray to the top-level kwave/ namespace. It's still buried at kwave/utils/kwave_array.py, which forces awkward imports for what's a primary user-facing class. (The original issue had broader scope, but most other classes are already at top level — only kWaveArray is the outstanding case.)
• Remove redundant arguments from simulation_options #339 — Deprecate the per-axis pml_x_size / pml_y_size / pml_z_size fields on SimulationOptions in favour of the unified pml_size (scalar or vector). The modern kspaceFirstOrder() already exposes only pml_size; this is internal-plumbing cleanup.

Originally bundled but reassessed

• Clean up duplicate code in kSpaceFirstOrder{2,3}D #257 (dedup kspaceFirstOrder2D.py / kspaceFirstOrder3D.py) — these are deprecated legacy entry points; refactoring them is not worthwhile when the plan is to remove them. Removed from this umbrella.
• [Enhancement] Update Recorder logic in kSim #471 (blank Recorder + kSensor) — the underlying API was tightened so that sensor.record must be a list[str], not a Recorder object. The original failure mode no longer applies. Removed from this umbrella.

How to use this issue

Pick either of the two listed items when you're already in the affected area. PRs should link Closes #N for the specific sub-issue they address. When both are closed, this umbrella can be closed too.