Phase 6: strip signature-restating docstrings; correct README/SETUP

- Collapsed Args:/Returns:/Raises: blocks that only restated the
  signature (364 lines): tektronix_base 48% -> ~20% doc density,
  helios_laser and uc480_camera likewise. Only docstrings whose entire
  body was those sections were touched.
- Preserved verbatim the comments that carry hardware knowledge the code
  can't express: uc480's USB split-transaction contention note (with its
  measured fps), the IS_ALLOW_STARTER_FW_UPLOAD segfault explanation, the
  QImage-copy rationale, and tektronix's NUMFRAMESACQuired warning.
- README: project structure, quick start, and every usage example now
  describe code that exists (they referenced hardware/bbd202.py,
  CoherentHOPSLaser, get_curve_binary, and 'python -m scanengine.app',
  none of which do). Added a headless-scan example and a read-a-scan-file
  example, since reuse without the GUI is the point of the refactor.
- SETUP: structure section defers to README instead of keeping a second
  stale copy; documents the vendored uEye SDK and the Genesis quarantine.
- ruff is now clean repo-wide: fixed the remaining raise-from, unused
  loop variables, placeholder f-strings, and a non-strict zip; the
  widget-layout semicolon idiom is an explicit config ignore rather than
  22 standing warnings.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

SETUP.md

@@ -91,11 +91,10 @@ lsusb | grep -i thorlabs
 **First-time setup:**
 ```bash
 # Run the stage test application
-python stage_test_app.py
+python bbd202_test_app.py
 
-# Enter your BBD203 serial number
-# Click "Connect" to test the connection
-# Use "Home All Axes" to verify operation
+# Set the serial port, click Connect (it now fails loudly if no bay
+# responds), then Home to verify operation.
 ```
 
 ### Helios Laser System
@@ -132,10 +131,15 @@ python -c "from pyftdi.ftdi import Ftdi; Ftdi.show_devices()"
 
 **First-time setup:**
 ```bash
-# Test laser connection
-python -c "from hardware.coherent_hops_laser import CoherentHOPSLaser; laser = CoherentHOPSLaser(); print('Connected:', laser.connect())"
+# Test the Genesis laser connection
+python tools/genesis_laser_control.py
 ```
 
+> Before changing any Genesis code, read
+> [docs/genesis_verification.md](docs/genesis_verification.md) — the two
+> implementations in the repo disagree on ADC scaling, LDD polarity, and
+> shutter behaviour, and only the bench can settle it.
+
 ### Tektronix Oscilloscope
 
 **Connection:**
@@ -228,65 +232,21 @@ Main window settings (geometry, last used values) are stored in Qt settings:
 
 ## Project Structure
 
-```
-scanengine-3/
-│
-├── scanengine/                    # Main application package
-│   ├── __init__.py
-│   ├── app.py                     # Main application entry point
-│   ├── main_launcher.ui           # Main launcher UI
-│   ├── new_scan_wizard.ui         # Scan wizard UI
-│   └── options.ui                 # Options dialog UI
-│
-├── hardware/                      # Hardware driver package
-│   ├── __init__.py
-│   ├── bbd202.py                  # ThorLabs stage controller
-│   ├── uc480_camera.py            # IDS/ThorLabs camera
-│   ├── tektronix_base.py          # Tektronix oscilloscope
-│   ├── coherent_hops_laser.py     # Coherent HOPS laser
-│   └── genesis_core.py            # Genesis laser core logic
-│
-├── scanning/                      # Scan planning package
-│   ├── __init__.py
-│   ├── sc3_scan_model.py          # Scan model
-│   └── stage_scan_plan_generator.py  # Scan path planning
-│
-├── tools/                         # Standalone executable tools
-│   ├── genesis_laser_control.py   # Standalone Genesis app
-│   └── genesis_laser_gui.py       # Alternative Genesis GUI
-│
-├── tests/                         # Test files
-│   ├── __init__.py
-│   ├── test_camera_integration.py
-│   ├── test_genesis_connection.py
-│   ├── test_genesis_protocol.py
-│   ├── test_rotated_aoi.py
-│   └── test_temperature_scaling.py
-│
-├── docs/                          # Documentation
-│   ├── hardware/                  # Hardware documentation
-│   │   ├── BBD203_CONNECTION_GUIDE.md
-│   │   ├── BBD203_Communications_Protocol.md
-│   │   ├── BBD203_DRIVER_README.md
-│   │   ├── HELIOS_DRIVER_README.md
-│   │   ├── GENESIS_LASER_README.md
-│   │   └── laser_control_implementation_guide.md
-│   └── protocols/                 # Protocol specifications
-│       ├── apt_communications_protocol.pdf
-│       ├── helios_comms_protocol.pdf
-│       └── thorlabs_mls_protocol.pdf
-│
-├── lib/                           # Binary libraries (not in git)
-│   ├── libueye_api64.so.3.82
-│   ├── ueye_loader.c
-│   └── ueye_loader.so
-│
-├── config.json                    # System configuration
-├── requirements.txt               # Python dependencies
-├── README.md                      # Project overview
-├── SETUP.md                       # This file
-└── LICENSE                        # License file
-```
+See the tree in [README.md](README.md#project-structure). In short: `core/`
+is the headless scan engine and file format (no PyQt6, no vendor SDKs),
+`hardware/` holds the Qt-free device drivers, `gui/` the shared PyQt6
+adapters and widgets, and the root `*.py` files are the runnable apps.
+
+## Vendored camera SDK (`lib/`)
+
+`lib/` is gitignored, so a fresh clone does not have it. The IDS uEye
+runtime (`libueye_api64.so.3.82`) must come from the IDS SDK installation
+matching the camera firmware on this rig.
+
+`lib/ueye_loader.{c,so}` is an `LD_PRELOAD` shim that dlopens
+`/usr/lib/libueye_api.so` before Python starts. Nothing in the repo
+references it and no launcher sets `LD_PRELOAD`, so whether it is still
+needed is an open question — see [KNOWN_ISSUES.md](KNOWN_ISSUES.md).
 
 ## Troubleshooting