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docs: move development notes to NOTES.md and describe the CLI in the README

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NOTES.md
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# IDE Setup (Windows)
## Layout
- Installed Intel Quartus Lite from https://www.intel.com/content/www/us/en/software-kit/825278/intel-quartus-prime-lite-edition-design-software-version-23-1-1-for-windows.html
- Installed Arduino IDE 2 `choco install arduino`
- `fpga/rtl/`: Verilog sources; `fpga/sim/`: testbenches; `fpga/src/`: Quartus project
- `arduino/strix/`: device firmware
- `arduino/strix_capture/`: characterization tool firmware, used by `tools/jitter.py`
- `arduino/strix_nina_passthrough/`: connects USB to the WiFi module's UART for flashing its firmware
- `arduino/libraries/`: `StrixFPGA` (FPGA boot, SPI access, embedded FPGA image), `VidorBoot` (vendored subset of Arduino's VidorPeripherals), and Arduino's `WiFiNINA`, `Arduino_SpiNINA` and `ArduinoBLE`, patched to drive the WiFi module through the FPGA's pin pass-through (see `arduino/libraries/STRIX-NINA-LIBRARIES.md`)
- `tools/`: `strix.py` command-line client, FPGA image converter, jitter and statistics experiments, API check
# Project Setup
## Development (Linux)
based on https://docs.arduino.cc/tutorials/mkr-vidor-4000/vidor-quartus-vhdl/
The toolchain is managed by [devbox](https://www.jetify.com/devbox): `arduino-cli`, Intel Quartus Prime Lite (Cyclone 10 LP only, through a Nix flake in `nix/`), Icarus Verilog, Rust, and [uv](https://docs.astral.sh/uv/) for the Python tools (`pyproject.toml`, `uv.lock`).
- New Project Wizard
- 'strix' for name and top level design entity
- Skip next screen
- Family, Device, Board Settings > Name filter: `10CL016YU256C8G`
- Finish
1. `devbox run setup`: install the Arduino SAMD core (libraries are vendored in `arduino/libraries/`)
2. `devbox run sim`: run the FPGA testbenches
3. `devbox run fpga`: build the FPGA bitstream (about 10 minutes)
4. `devbox run image`: embed the bitstream in the `StrixFPGA` library
5. `devbox run build`, then `devbox run upload`: build and flash the firmware (`PORT` defaults to `/dev/ttyACM0`)
6. `devbox run api-check`: end-to-end check of the USB API
7. `devbox run strix <command>`: command-line client over USB (see the README)
- Import Pin Settings:
- Menu > Assignments > Import Assignments > vidor_s_pins.qsf
- from https://github.com/vidor-libraries/VidorFPGA/blob/master/constraints/MKRVIDOR4000/vidor_s_pins.qsf
Serial access requires membership in the `dialout` group. If a firmware leaves the board unable to stay on USB, enter the bootloader: hold reset while plugging in, release, then tap reset once quickly. For characterization, flash the capture tool with `devbox run upload-capture` and use `devbox run jitter <freq|rings|sweep|output|health|stats|amp|pairs>`. `devbox run onod-build` builds the onod3000 test suite used by `jitter output` and `api-check`.
### WiFi module firmware
BLE needs NINA firmware 3.0.0 or newer (the board shipped with 1.0.0). To flash Arduino's [nina-fw](https://github.com/arduino/nina-fw/releases) `NINA.bin`:
1. Flash the passthrough: `devbox run -- arduino-cli compile -u -p /dev/ttyACM0 --fqbn arduino:samd:mkrvidor4000 --libraries arduino/libraries arduino/strix_nina_passthrough`
2. `devbox run -- uv run esptool --chip esp32 --port /dev/ttyACM0 --baud 115200 write-flash 0 NINA.bin`
3. Flash the STRIX firmware again (`devbox run upload`); `wifi probe` reports the module firmware version.
The passthrough forwards reliably at 115200 baud, not at 460800.

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README.md
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The USB, HTTP and BLE API is documented in [arduino/strix/API.md](arduino/strix/API.md).
## Layout
## Command-line client
- `fpga/rtl/`: Verilog sources; `fpga/sim/`: testbenches; `fpga/src/`: Quartus project
- `arduino/strix/`: device firmware
- `arduino/strix_capture/`: characterization tool firmware, used by `tools/jitter.py`
- `arduino/strix_nina_passthrough/`: connects USB to the WiFi module's UART for flashing its firmware
- `arduino/libraries/`: `StrixFPGA` (FPGA boot, SPI access, embedded FPGA image), `VidorBoot` (vendored subset of Arduino's VidorPeripherals), and Arduino's `WiFiNINA`, `Arduino_SpiNINA` and `ArduinoBLE`, patched to drive the WiFi module through the FPGA's pin pass-through (see `arduino/libraries/STRIX-NINA-LIBRARIES.md`)
- `tools/`: FPGA image converter, jitter and statistics experiments, API check
`tools/strix.py` talks to the device over USB; run it with `devbox run strix <command>` or `uv run tools/strix.py <command>`. It finds the board by its USB ID (override with `--port` or `STRIX_PORT`).
## Development (Linux)
| Command | Does |
|---|---|
| `id`, `health`, `amp`, `get` | Prints the device's reply |
| `stats [--reset]` | Prints the statistics, or restarts them |
| `set KEY VALUE` | Changes a setting (keys in the API documentation) |
| `entropy N [--out FILE]` | N entropy bytes as hex, or binary into a file |
| `watch stats\|amp` | Prints every new trial until Ctrl-C |
| `gcp [--log FILE] [--full] [--seconds N]` | Follows the per-second GCP-format trials |
| `send LINE` | Sends any command line and prints the reply |
The toolchain is managed by [devbox](https://www.jetify.com/devbox): `arduino-cli`, Intel Quartus Prime Lite (Cyclone 10 LP only, through a Nix flake in `nix/`), Icarus Verilog, Rust, and [uv](https://docs.astral.sh/uv/) for the Python tools (`pyproject.toml`, `uv.lock`).
1. `devbox run setup`: install the Arduino SAMD core (libraries are vendored in `arduino/libraries/`)
2. `devbox run sim`: run the FPGA testbenches
3. `devbox run fpga`: build the FPGA bitstream (about 10 minutes)
4. `devbox run image`: embed the bitstream in the `StrixFPGA` library
5. `devbox run build`, then `devbox run upload`: build and flash the firmware (`PORT` defaults to `/dev/ttyACM0`)
6. `devbox run api-check`: end-to-end check of the USB API
Serial access requires membership in the `dialout` group. If a firmware leaves the board unable to stay on USB, enter the bootloader: hold reset while plugging in, release, then tap reset once quickly. For characterization, flash the capture tool with `devbox run upload-capture` and use `devbox run jitter <freq|rings|sweep|output|health|stats|amp|pairs>`. `devbox run onod-build` builds the onod3000 test suite used by `jitter output` and `api-check`.
### WiFi module firmware
BLE needs NINA firmware 3.0.0 or newer (the board shipped with 1.0.0). To flash Arduino's [nina-fw](https://github.com/arduino/nina-fw/releases) `NINA.bin`:
1. Flash the passthrough: `devbox run -- arduino-cli compile -u -p /dev/ttyACM0 --fqbn arduino:samd:mkrvidor4000 --libraries arduino/libraries arduino/strix_nina_passthrough`
2. `devbox run -- uv run esptool --chip esp32 --port /dev/ttyACM0 --baud 115200 write-flash 0 NINA.bin`
3. Flash the STRIX firmware again (`devbox run upload`); `wifi probe` reports the module firmware version.
The passthrough forwards reliably at 115200 baud, not at 460800.
`gcp` prints one line per second: UTC time, second number, the four 200-bit sums, Stouffer Z, Z², and the cumulative Z² − 1 with its p = 0.05 envelope (`*` when outside). `--full` tracks the full-rate trials instead. It reconnects after USB dropouts and fills missed seconds from the device's 60-second history. `--log` appends GCP-style CSV rows, `13,<unix time>,<UTC date-time>,<g0>,<g1>,<g2>,<g3>` (empty for unhealthy generators), after a `12,gmtime,Date/Time,g0,g1,g2,g3` header.
## TODO

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arduino/strix/API.md
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The firmware speaks a line protocol over the board's USB serial port (115200 baud setting, ignored by native USB). Send one command per line. Every reply is a single JSON line, except `entropy`. Errors look like `{"error":"..."}`, and settings changes confirm with `{"ok":true}`.
`tools/strix.py` (`devbox run strix <command>`) wraps the USB protocol. `strix gcp [--log file.csv] [--full]` follows the per-second trials with a live cumulative Z² − 1 and its p = 0.05 envelope, reconnects after USB dropouts and fills gaps from the device's history. The log has GCP-style rows: `13,<unix time>,<UTC date-time>,<g0>,<g1>,<g2>,<g3>` (200-bit sums, empty for unhealthy generators), after a `12,gmtime,Date/Time,g0,g1,g2,g3` header.
`tools/strix.py` wraps this protocol (see the README).
## Commands