rugnux: measure the ice in the first pass, and always find its own spots

Ice handling was gated on a measurement the run only made AFTER the images had
been processed, so the per-image pass could not use it. The flagging therefore
ran unconditionally: ice-band spots were ordered last in the --max-spots budget
and held out of the indexer seed and the geometry refinement on every crystal,
iced or not. The eleven bands are fixed geometry holding 16-26 % of the unique
reflections whether or not there is ice, so on a clean crystal that discards a
fifth of the spots - the strongest first - for nothing. Measured on a crystal
whose gate never fires, that moved the merged data by a mean of 0.85 sigma
against a run-to-run floor of 9.3e-5.

Measure it in the first pass instead. That pass already looks at ~100 images
spread over the sweep, and it already stops at the spot finder, so it sees the
azimuthal profile for the smooth channel and the unfiltered connected components
for the spot channel. Both counts SpotAnalyze takes are pre-filter, so pooling
them there is the run's own verdict, reached before anything has been discarded
and in time for the pass that acts on it. Where the sample sees no ice, the run
indexes on the ice-band spots too.

It has to be the whole sample: the spot channel is a ratio pooled over images,
because one frame carries a handful of control spots. A per-image gate is not an
alternative - two of the crystals whose indexing this rescues fire on that
channel alone, at profile scores of 1.12 and 1.22, so gating per image on the
profile score would drop exactly the cases that matter.

This also removes the first-pass spot reuse, and with it --redo-rotation-spots
and the reuse path. Finding the ~100 first-pass spots costs little, and reusing
was actively wrong here: the stored spots were found online at the acquisition's
threshold and have already had their ice-band entries ordered last and dropped
by its spot budget, so counting ice from them under-reads it by construction,
and the lattice search never saw the spot-finding settings at all. It also
removes the need for the machinery that re-found spots whenever a spot-finding
option was named, which made those options impossible to A/B.

IndexAndRefine cached index_ice_rings at construction, which happens before the
first pass; it holds a reference to the experiment, so it now reads the setting
where it uses it.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

docs/RUGNUX.md

@@ -34,9 +34,11 @@ scale with the thread count (`-N`).
 
 ## Input and output
 
-**Input** is a single Jungfraujoch HDF5 master file (NXmx-based). If the dataset already contains
-stored spot lists, two-pass rotation indexing can reuse them instead of re-running spot finding on
-the first pass.
+**Input** is a single Jungfraujoch HDF5 master file (NXmx-based). Spots are always found by `rugnux`
+itself, including for the two-pass rotation first pass — the spot lists a dataset may already carry
+were found online, at the acquisition's threshold and with its ice-band spots already discarded, so
+reusing them would hide the spot-finding settings from the lattice search and stop the run measuring
+its own ice.
 
 **Output** (controlled by `-o, --output-prefix`, default `output`):
 
@@ -240,7 +242,6 @@ rotation explicitly and pick the pass or lattice.
 | `-r, --refine <txt>` | Geometry refinement: `none` \| `orientation` \| `beam_and_lattice` (default) \| `flex` (try all three per image, keep whichever indexes the most spots; alias `multi`) |
 | `-R, --two-pass-rotation[=num]` | Two-pass offline rotation indexing (default for goniometer data; optional first-pass image count, default 100) |
 | `--single-pass-rotation[=num]` | Online-like single-pass rotation indexing (optional min angular range, deg) |
-| `--redo-rotation-spots` | Redo spot finding for the two-pass rotation first pass |
 | `--force-rotation-lattice <vec>` | Force rotation lattice (9 floats, Å), skipping the first pass |
 | `--rotation-no-postrefine` | Rotation: disable the default-on two-pass geometry post-refine (see the rotation section) |
 | `--refine-geometry[=N\|off]` | Stills: extra first pass that bundle-adjusts the shared beam/distance/cell from N strongly-indexed frames (default 200) then re-indexes; default ON for stills with a reference cell (`-C` / `-z`), `=off` disables |