Stabilize CLI, modularize commands, migrate packaging to uv + pyproject.toml

[Copilot]

Several CLI commands were broken or incomplete, core search logic had a string/sequence confusion bug, and the project used a legacy setup.py + requirements.txt stack. This PR addresses all three areas.

Core bug fixes

• search_by_ids_in_flora: a plain str was iterated as a character sequence — "geo" would match inside query string "geo-nuts". Fixed by normalizing to [str] before the membership test.
• Flora.__init__: remote flora called self.workdir before it was set; plain str paths were rejected. Both fixed.
• Flora._convert_to_herb: Herb was constructed without base_path, falling back to a config file lookup that fails in CI. Now passes self.workdir / id.
• upload / validate: used __CWD__ = Path(__file__).parent (the package directory, evaluated at import time) instead of Path.cwd(). Fixed.
• validate: called MetaData() with no args (raises); MetaData.validate() returned None — CLI iterated it. Implemented a real structured return: {"data": [{"path": {...}, "name": {...}}]}.
• add: implementation was cut off at a # TODO. Completed — fetches remote metadata and calls fl.add(Herb(metadata)).
• Broad Exception(...) raises replaced with ValueError, FileNotFoundError, TypeError, ConnectionError, click.ClickException.

CLI restructuring

Split the 600-line monolithic command.py into focused modules:

Module	Commands
dataherb/cmd/flora.py	search, download, add, remove
dataherb/cmd/dataset.py	create, upload, validate
dataherb/cmd/configure.py	configure
dataherb/cmd/serve.py	serve

command.py is now ~50 lines — a thin registration file using dataherb.add_command(...).

Tests

35 new tests (43 total):

• tests/core/test_search.py — exact-match, multi-id, empty, and the string-safety regression
• tests/core/test_metadata.py — MetaData.load, validate (success/error/missing), create
• tests/test_cmd/test_cli.py — CLI regression via CliRunner: search, validate, upload abort
• tests/integration/test_flora.py — add/remove roundtrip, unknown-id returns None, duplicate-ID guard

Packaging migration

Replaced setup.py + requirements*.txt with pyproject.toml (hatchling backend) and a uv.lock lockfile.

# install project + dev deps
uv sync --extra dev

# run tests
uv run pytest

CI updated to use astral-sh/setup-uv@v5 instead of setup-python + manual pip installs.

Also fixed a distutils.dir_util.copy_tree import in save_mkdocs.py that broke on Python 3.12 (module removed); replaced with shutil.copytree(..., dirs_exist_ok=True).