Config labels in every output, independent facet scales, green CI

[degoldschmidt]

Closes #2.

Config labels set in experiment.yaml reached config.used.yaml but not the exported
tables or the figures. The bulk of that was already fixed in a39a78d (on main since
2026-07-29, after the issue was filed against 2778288); this branch finishes the job,
takes care of a readability problem the fix exposed, and gets CI green again.

Name the substrates in the two-choice figure (9fc8fd6)

substrate_comparison() was the last output ignoring the configured labels: its legend
hardcoded left / right, so metadata.substrates never reached it. Each side is now
named after the substrate it holds, falling back to left / right when the experiment
records no labels — or the same label on both sides, where the side is the only thing
telling the two boxes apart.

The same figure ordered conditions alphabetically while every other figure uses the
experiment sequence; it now shares ordered_condition_labels(), which additionally
learns to group by the order column itself so an unlabelled experiment (grouping on the
numeric code) no longer trips over a duplicate column.

Stack facets and scale each to its own data (894dd6c)

Faceted figures shared one y-axis, so a substrate the flies barely touched collapsed onto
the baseline beside one they fed on heavily. Facets now scale independently and stack
top-to-bottom, with the shared condition axis drawn once under the bottom facet.

Two new options restore the old behaviour: plotting.facet_share_y: true for a single
shared scale (magnitudes comparable across facets, at the cost of the smaller one), and
plotting.facet_layout: columns for the side-by-side arrangement.

This exposed a latent bug in the significance brackets, fixed here: the stack was laid
out in axes fractions computed before the y-limit was grown to fit it, so with 5
conditions (10 brackets) it overshot 1.0 — drawing over the facet title — while squashing
the data into the lower third. The layout is now solved in final fractions and the step
compresses into a bounded band, so brackets stay inside the axes and the data always
keeps at least half the height. On independent axes brackets anchor to their own facet's
data rather than the tallest, which would otherwise re-inflate the axis the independent
scaling was meant to keep tight.

Type-check the GUI layer without the gui extra (12135c7)

CI has been red since 2026-07-30, unrelated to the above. It syncs with
uv sync --frozen, which installs the dev group but not the optional gui one, so
every Qt accessor degrades to Any and reading a value back out of a widget trips
warn_return_any. Locally PySide6 is installed, the accessors are typed, and mypy is
silent — which is why this only ever showed up on the runner. The flypad.gui.* override
already exists to make the layer check identically with or without the extra;
warn_return_any was the one setting missing from it.

Verification

End-to-end on the shipped data/sample/20240215 fixture:

uv run flypad run data/sample/20240215 -c configs/example_experiment.yaml -o /tmp/retest \
  --set 'metadata.substrates=["10% yeast", "20mM sucrose"]' \
  --set 'metadata.conditions=["1st condition", "2nd condition"]'

The configured names appear in per_fly / events / per_condition / comparisons
(CSV and Parquet), the box-plot tick labels, the facet titles, the substrate-figure
legend, and the raster and time-course legends.

• 240 tests pass locally (with the gui extra installed).
• Reproducing the runner's environment (UV_PROJECT_ENVIRONMENT + uv sync --frozen):
  ruff, ruff format, mypy and pytest all pass — 227 passed, test_gui skipped for the
  absent qtpy.
• 12 new tests cover the substrate legend and its fallbacks, condition ordering, facet
  layout / independent scaling, the x-axis being captioned once, and the bracket stack
  staying inside the axes.

Docs

docs/configuration.md gains a section on how metadata.conditions / .substrates apply
positionally and which outputs they reach, versus the figure-only
plotting.condition_labels rename, plus a table for the two new faceting options.
CHANGELOG.md gains an [Unreleased] section.