fix: compute confocal excitation at the excitation wavelengths; refactor PSF pipeline

[tlambert03]

This is the PR #161 and #162 were prep for. It started as a one-line question: does point-scanning confocal compute its PSF at the excitation or the emission wavelength? Turns out it was the emission wavelength... for both the excitation spot and the detection PSF. Fixing that properly meant pulling apart how modalities, channels and PSFs fit together, so this restructures the simulation → modality → PSF pipeline.

How images are formed now (widefield is just the case where the excitation is uniform):

• system PSF = excitation spot × detection PSF. The spot is computed at the excitation wavelengths (several spots for multiple lasers/broadband sources, binned by width via the new Settings.excitation_bin_width_nm); the detection PSF is computed at the emission wavelengths and, for confocal, convolved with an anti-aliased pinhole mask (so small pinholes don't snap to whole pixels).
• brightness is separate from PSF shape. Each channel × fluorophore gets a detected photon rate (photons/s per fluorophore) and the PSFs carry only shape. For confocal, saturation (E / (1 + sE)) is applied locally across the spot, so it's strongest at the center. A nice side effect: changing laser power no longer recomputes PSFs.
• (confocal) pinhole size in Airy units is defined at the emission filter band center, so one channel has one physical pinhole (rather than a different pinhole per emission wavelength bin). Confocal.airy_unit_wavelength_nm overrides that.

Internally: modalities pick an illumination (WidefieldIllumination/FocusedIllumination) and a detection (CameraDetection/PinholeDetection) from a new private _optics.py, and Simulation hands them a ChannelFluorescence per channel × fluorophore (absorption rate and detected fraction by wavelength) instead of an xarray of emission rates.

Coming next: laser channels (LASER_488 etc.) and updated confocal examples/docs, then acquisition tracks (sequential vs. simultaneous channels).

Breaking changes

• all confocal output changes (excitation wavelength, pinhole definition).
• filtered_emission_rates() / emission_flux() apply saturation by default for every modality (new saturate= keyword).
• removed microsim.psf.cached_psf, Modality.psf(), and point_scanning; Modality.render() has a new signature.
• cached PSF arrays are read-only (make_psf returns a copy).
• Identity output follows settings.float_dtype (float32 by default).
• Confocal.pinhole_au must be at least 0.05 AU: a fully closed pinhole isn't allowed (on main, pinhole_au=0 meant a one-pixel pinhole; now it would pass no light at all).
• confocal warns for channels without a band-limited emission filter.
• new fields on Confocal and Settings, so JSON saved with this version won't load in older ones.
• PSF disk cache layout changed (old cached PSFs are just orphaned, not misread).

Speed is the same as main within noise; peak memory is up ~0.1-0.2 GB (3-6%) on the README example.

Known limitations / follow-ups

• pinhole throughput depends on pixel size. The pinhole mask area is now exact, but the emission PSF is still sampled at the voxel size, so at coarse pixels the light through a small pinhole is off: at 0.5 AU, -12% at dx=0.1 µm and +27% at 0.2 µm (vs 0.02 µm). The fix is probably computing the detection PSF on a finer grid before the pinhole convolution.
• the confocal PSF radius is a fixed 8 AU (unchanged from main). It doesn't account for pinhole size or depth, so it clips a bit of out-of-focus excitation in thick volumes and some light from large pinholes.

[codecov]

Codecov Report

❌ Patch coverage is 98.03922% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.14%. Comparing base (1773a2e) to head (9fc40dc).

Files with missing lines	Patch %	Lines
src/microsim/psf.py	90.90%	3 Missing ⚠️
src/microsim/schema/optical_config/config.py	85.71%	2 Missing ⚠️
src/microsim/schema/simulation.py	95.23%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #163      +/-   ##
==========================================
+ Coverage   88.26%   89.14%   +0.87%     
==========================================
  Files          49       51       +2     
  Lines        3316     3483     +167     
==========================================
+ Hits         2927     3105     +178     
+ Misses        389      378      -11     

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