Refresh documentation screenshots for the night theme

Regenerate 110 GUI captures, centralize tutorial references, and retire historical interface assets. Preserve original case-study measurements as lossless crops with source provenance.

Extend the existing CaptureSpec registry and popup/controller paths for menus and tutorials. Selected popup captures now overwrite existing files; dropdown captures preserve transient stacking. Application runtime code is unchanged.

Validation: all captures completed on Linux/Xvfb; visual image and rendered-page review; 134 local image references resolve; 13 source crops are pixel-exact; clean Sphinx build matches baseline warning set; Ruff, Black 22.10, syntax, and whitespace checks pass.

Author: kevin-m-dean

docs/AGENTS.md

@@ -130,10 +130,12 @@ conda run -n navigate python docs/capture_gui.py --list
 
 - Key selectors:
   - `--all`
-  - `--group <group>`
+  - `--group <group>` (including `menus` and `tutorials`)
   - `--capture <id>`
   - `--manifest <json>`
   - `--configurator-only` (compatibility shortcut)
+- Selected captures overwrite existing files, including popup screenshots.
+- For full unattended captures, use Linux/X11 with Xvfb; see `docs/SCREENSHOTS.rst`.
 - The capture path expects `mss` in docs dependencies; do not add a PIL fallback.
 - For UI pages that are not fully rendered, increase settle timing:
   - `--passes <n>`

docs/SCREENSHOTS.rst

@@ -0,0 +1,44 @@
+Refreshing documentation screenshots
+====================================
+
+Run the capture script from the repository root with the Navigate environment
+and documentation dependencies installed::
+
+    python docs/capture_gui.py --list
+    python docs/capture_gui.py --all
+
+All selected captures replace their previous files, including popups. The
+``menus`` and ``tutorials`` groups cover the menu walkthrough and the feature,
+multicamera, and ilastik examples. Use ``--group``, ``--capture``, or ``--manifest``
+for a smaller refresh. Outputs belong in ``docs/source/images/``; tutorial pages
+should reference these shared images instead of keeping local copies.
+
+For a complete unattended capture, use Linux with an X11 virtual display::
+
+    xvfb-run -a -s "-screen 0 3200x2200x24" \
+        python docs/capture_gui.py --all --passes 3 --delay-ms 100
+
+The script uses synthetic hardware and illustrative settings. It does not run
+an experiment. Use a disposable user profile when installed plugins or personal
+configuration could affect screenshots. Native macOS menus can block Tk's event
+loop or expose no capturable bounds; capture menus on X11. On an interactive
+desktop, keep other windows and system overlays away during capture.
+
+Review every generated image for clipping, blank controls, or overlapping
+windows. Then build the documentation::
+
+    conda run -n navigate make -C docs html -j 15
+
+Check image references throughout ``docs/source/``, including case studies and
+contributor tutorials, and remove unused historical GUI images. A successful
+capture run alone does not verify that every documentation page uses it.
+
+Preserved case-study results
+---------------------------
+
+``source/images/case-studies/`` contains the original beam and tissue images,
+autofocus plots, segmentation result, and CSV example with historical GUI
+chrome removed. These are lossless crops, not new measurements or simulations.
+``case_study_image_sources.json`` records the source commit, original file, and
+crop bounds so each image can be reproduced from Git history. Do not replace
+experimental results with synthetic screenshots when refreshing the interface.