Adopt the analysis-workflow plugin; commit notebook outputs; zarr

[Marius1311]

Changes

• Agent conventions come from the analysis-workflow plugin. .claude/settings.json enables it (via the quadbio/claude-plugins marketplace), pixi.toml depends on its package (tag v0.1.0), and FilePaths.ROOT comes from its main_checkout() instead of a local resolver. AGENTS.md points at the plugin instead of restating conventions; README gains a short "Working with coding agents" section.
• Notebook outputs are committed. The nbstripout filter, its install step and the CI check that rejected outputs are gone.
• Zarr instead of h5ad in the examples; *.zarr ignored.
• data/<dataset>/results/ is a notebook's own outputs, prefixed with the notebook's stem. data/ is ignored except its READMEs and placeholders (AGENTS.md already claimed this; only extensions were ignored).
• Task-output rules in .gitignore: outputs/, logs/ and re-included results/ evidence.
• REVIEW_GUIDE.md for GitHub review agents, generic part from the plugin.

The lock re-solve also floats a few packages (spatialdata 0.7.3 → 0.8.0, dask, numba, ome-zarr).

Next: converting the template to cruft, so repos can pull template updates with cruft update, as a separate PR.

🤖 Generated with Claude Code

[Marius1311]

Good overall, some duplication left. Is the cruft setup in already?

[Marius1311]

is it a plugin or a skill? I thought a plugin bundles several skills?

[Marius1311]

A plugin. A plugin is the installable unit and can bundle any number of skills, plus hooks, agents and MCP servers. This one bundles one skill (also called analysis-workflow) and the guard hooks. The Python package is separate: pixi installs it, not Claude. The README now says "plugin (a skill plus guard hooks)". a8ce86b

[Marius1311]

Looks like we're repeating this three times, here, in the skill, and in the agents.md file

[Marius1311]

Agreed, removed from both the README and AGENTS.md. The skill owns it; AGENTS.md now only lists what the plugin owns and points there. a8ce86b

[Marius1311]

Consider how much of this is needed, given what's in the skill now.

[Marius1311]

Cut to the install step, which is the one thing the skill can't tell a human: it only loads after installation. Dropped the package sentence (pixi.toml shows it) and the REVIEW_GUIDE.md pointer (AGENTS.md has it). a8ce86b

[Marius1311]

Also in a8ce86b: the data/ layout had three copies in the template. It now lives once for humans, in the README; data/example_dataset/README.md and the sample notebook point there. The skill keeps its own copy for agents, since humans don't read the skill. AGENTS.md also drops the notebook-naming line (README owns it) and the worktree commands (the skill and its hook own them).

Cruft: not yet. It's planned as its own PR once this one merges, so its diff (moving everything under {{ cookiecutter.project_name }}/) stays separate from this content change.