Split analysis/ by dataset, then by topic

.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "analysis-workflow",
-  "version": "0.4.0",
+  "version": "0.5.0",
   "description": "Conventions for analysis repos where humans (notebooks) and coding agents (scripts) work side by side: one task per session, worktree and directory; worktree-safe output paths; additive write-back to AnnData zarr working objects. Ships a skill, guard hooks and the analysis_workflow Python package.",
   "author": {
     "name": "quadbio"

README.md

@@ -24,7 +24,7 @@ branches from `origin`'s default branch but runs on the main checkout's environm
 claude --worktree <task>
 ```
 
-1. The agent works on that worktree's branch, in a new task directory `analysis/<topic>/<task>_vN/`; a later
+1. The agent works on that worktree's branch, in a new task directory `analysis/<dataset>/<topic>/<task>_vN/`; a later
    answer to the same question gets the next version, in a new session. Earlier task directories are never edited.
 2. It asks you which working object is current and agrees what the task delivers (by default your `deliverables`
    setting), then works in scripts; outputs go to the task directory.

hooks/guard_task_layout.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 """Keep every task directory in the template's layout.
 
-A task directory (`analysis/<topic>/.../<name>_vN/`) holds at its top only what the task template holds
+A task directory (`analysis/<dataset>/<topic>/.../<name>_vN/`) holds at its top only what the task template holds
 (`skills/analysis-workflow/assets/task_template/`), the output directories of `task_paths` and a task-local
 environment. Its README's title is the directory's name, and its other headings are the template README's, all of
 them and in order. Both are read from their sources, the template and `paths.py`, so a change there is a change here.

hooks/session_context.md

@@ -1,7 +1,7 @@
 This repository follows the analysis-workflow conventions. Load the `analysis-workflow` skill before writing
 analysis code, outputs or data. Always:
 
-1. One task = one session = one git worktree = one directory `analysis/<topic>/.../<name>_vN/`. A new task
+1. One task = one session = one git worktree = one directory `analysis/<dataset>/<topic>/.../<name>_vN/`. A new task
    directory needs a new session, started with `claude --worktree <name>` in the main checkout.
    Analysis only moves forward: earlier task directories are never edited, fixed or updated.
 2. Every output path comes from `task_paths(__file__)` (package `analysis_workflow`); never a bare relative path.

skills/analysis-workflow/SKILL.md

@@ -35,8 +35,11 @@ Elsewhere:
 
 ## Two lanes
 
-Humans work in notebooks, flat under `analysis/<topic>/`, writing to `data/<dataset>/results/` and
-`figures/<topic>/`; notebook outputs are committed. Agents work in task directories, with scripts.
+`analysis/` is split by dataset, then by broad topic: `analysis/<dataset>/<topic>/`, with the dataset level even when
+there is one dataset. Topics, such as `preprocessing/`, `annotation/` or `spatial/`, can mostly be worked on in any
+order. Humans work in notebooks, flat under a topic, writing to `data/<dataset>/results/` and
+`figures/<dataset>/<topic>/`; notebook outputs are committed. Agents work in task directories under a topic, with
+scripts.
 
 ## Tasks
 

skills/analysis-workflow/assets/task_template/README.md

@@ -23,7 +23,7 @@ here too. -->
 <!-- The actual files, not concepts: this is what makes the task re-runnable. -->
 
 - Working object: `data/<dataset>/processed/.../<object>.zarr`, and the label keys used
-- Other artifacts consumed: `analysis/<other_task>/outputs/<file>`, `data/<dataset>/processed/<file>`
+- Other artifacts consumed: `analysis/<dataset>/<topic>/<other_task>/outputs/<file>`, `data/<dataset>/processed/<file>`
 
 ## Write-back