Update package structure to be installable #78

Background

The codebase imports its modules under the literal top-level name src (e.g. from src.dataset_tools.cli import cli), and the packaging entry points follow suit (ami-dataset = "src.dataset_tools.cli:cli"). After the Poetry→uv migration (#68), the wheel ships src/ and this works for editable installs and even for a non-editable pip install (verified by building the wheel and importing src.dataset_tools.cli from outside the repo).

It works, but src is not a good distribution package name:

• src is a generic name. In a shared environment it can collide or merge (implicit namespace packages) with any other project that also ships a top-level src.
• src/ is conventionally a layout container, not the package itself. The standard src-layout puts a single importable package one level down (src/<package>/) and imports it by name (<package>.…), never src.….
• pip install ami-ml currently exposes a package called src, which is surprising for any downstream consumer.

This aligns the repo with the standard src-layout used elsewhere in the lab.

Goal

Rename the package so the project installs cleanly and is imported as ami_ml:

• Move the modules under a single package: src/ami_ml/{dataset_tools,classification,localization}/
• from src.dataset_tools import … → from ami_ml.dataset_tools import …
• Packaging: [tool.hatch.build.targets.wheel] packages = ["src/ami_ml"]
• Update the entry points (ami-dataset, ami-classification), the tests (tests/ imports), and the flake8 per-file-ignores paths.

Sketch

mkdir -p src/ami_ml
git mv src/dataset_tools src/classification src/localization src/ami_ml/
# add src/ami_ml/__init__.py
grep -rl --include='*.py' --include='*.sh' '\bsrc\.' . | xargs sed -i 's/\bsrc\./ami_ml./g'
# then hand-fix: pyproject entry points + packages, flake8 per-file-ignores, any string refs

git mv is preferable to a Hatchling sources path remap: with the directory actually named ami_ml, both editable and wheel installs resolve ami_ml for free, and there's no dev/wheel import-name mismatch. (A build-time remap was tested and is fragile — it still forces the same import rewrite, so it buys nothing.)

Sequencing

This rewrites nearly every import line, so it should land after the in-flight PRs that heavily touch src/ (#74, #69) to avoid rebase conflicts.

Notes

• Not a blocker for Migrate dependency management from Poetry to uv #68 — the current src packaging is verified working; this is a correctness/cleanliness follow-up.
• Verify after: uv build --wheel, install the wheel non-editable in a clean venv, ami-dataset --help + import ami_ml.dataset_tools, and uv run pytest tests/.