Fix the broken Docker build and remove dead root config

[bardhh]

The CPU container the README tells people to build does not build. Both Dockerfiles fail on their uv line, each in a different way:

.devcontainer/Dockerfile:43    uv pip install .
  -> error: No virtual environment found; run `uv venv` ... or pass `--system`

Dockerfile:48                  uv pip install --system --no-root .
  -> error: unexpected argument '--no-root' found

--no-root is a uv sync flag, not a uv pip install one, and uv refuses to install into the system interpreter unless you ask it to with --system. The two files started as copies of each other and drifted, so only one is referenced by docker-compose.yml and neither works.

What this does

Consolidates onto the root Dockerfile and fixes it. The install is now uv pip install --system ., and the source is copied before the install runs. That second part matters more than it looks: the version comes from src/cbfkit/VERSION through [tool.setuptools.dynamic], and setuptools treats a missing version file as a warning rather than an error, so installing from pyproject.toml alone quietly produced an empty cbfkit 0.0.0. docker-compose.yml now points at the surviving file, which also makes it symmetric with how gpu.Dockerfile was already referenced.

Bringing COPY . . back onto the live path makes the build context weight real, so .dockerignore got tighter: generated media, prose directories and local tool state are excluded, and the mypy_cache entry that never matched the actual .mypy_cache is fixed. That one directory was about 200 MB on its own. The context drops from 405 MB to 11 MB. README.md and LICENSE stay in, since setuptools reads both for wheel metadata.

Two files are deleted because they do nothing:

• .gitattributes has been empty since 6e08796, two years ago. An empty one has no effect.
• .devcontainer/devcontainer.json is superseded by .devcontainer/cbfkit-container/, which is what the README's dev-container instructions already name. The nested one also carries a debug config the top-level one lacks.

Finally, two descriptions that had drifted from their code. conftest.py's docstring claimed it configured mypy, ruff and bytecode caches plus XLA memory settings; it does none of those. .env.example advertised MYPY_CACHE_DIR, RUFF_CACHE_DIR and PYTHONPYCACHEPREFIX, none of which can work from a .env: the first two are separate processes that never load the file, and Python reads the third at interpreter startup, before conftest.py runs. JAX_ENABLE_X64 was the file's only uncommented line and is already set in src/cbfkit/__init__.py. The file now says plainly which variables work and which have to be exported in your shell.

Verification

pytest -m "not slow" tests gives 492 passed, 4 skipped. black and ruff are clean on conftest.py. docker-compose.yml parses and both services resolve. Nothing references the deleted paths. The files setuptools needs (pyproject.toml, uv.lock, README.md, LICENSE, VERSION, py.typed, and all seven codegen .j2 templates) survive the new .dockerignore.

The container build itself is not verified. I had no Docker daemon available, so the two uv fixes were checked by running the exact invocations against uv 0.9.12 rather than through a real build. One assumption is worth naming: --system requires the base image's Python not to be PEP 668 externally-managed. ros:humble-ros-base-jammy is Ubuntu 22.04, which predates that marker, so it should be fine. Worth confirming before merge:

docker compose -f .devcontainer/docker-compose.yml build cbfkit

Since this build appears to have been broken for some time, there may be a second failure sitting behind the first.