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Flatten pipe/flow: update docs paths, collection, modkey, and agent instructions

Goal

Update all documentation, docs collection paths, modkey bibliography format, CLAUDE.md files, agent instructions, and spec docs to reflect flow-only addressing. No pipe concept, no derivative field.

Context

Prior tasks removed pipe from: registry, MCP functions, CLI, projio wrappers. This is the final cleanup — update everything that references the old pipe/flow model. The derivative directory is always derivatives/{flow_name}/ (implicit).

Prompt

Update all documentation and agent-facing content for flow-only addressing.

1. Docs collection paths (packages/pipeio/src/pipeio/docs.py)

Update docs_collect(): - Old target: docs/pipelines/{pipe}/{flow}/ - New target: docs/pipelines/{flow}/ - Mod docs: flow-local docs/mod-{mod}.md → docs/pipelines/{flow}/mods/{mod}.md - Notebooks: docs/pipelines/{flow}/notebooks/nb-{name}.html and .md - Scripts: docs/pipelines/{flow}/scripts/{script}.py (NEW — copy rule scripts for site display) - Remove any entry.pipe references — use entry.name for the flow

Update docs_nav(): - Nav structure: flat docs/pipelines/{flow}/ (no pipe grouping level)

2. Modkey bibliography (packages/pipeio/src/pipeio/mcp.py)

Update mcp_modkey_bib(): - Old citekey: pipe-{pipe}_flow-{flow}_mod-{mod} - New citekey: {flow}_mod-{mod} - Update title and note fields - This is a breaking change for existing citations — acceptable

3. Agent instructions (src/projio/init.py)

Update _generate_claude_md(): - Tool routing table: remove all pipe from examples - Notebook workflow section: (pipe, flow, name) → (flow, name) everywhere - Remove any mention of "pipe" as a concept

4. Spec docs (docs/specs/pipeio/)

Update: - notebook.md — remove pipe from examples, YAML schemas, CLI commands - mcp-tools.md — update all function signatures - cli.md — update CLI command signatures - scaffolding.md — update flow new examples - overview.md — remove pipe terminology, explain flow = unit of work, derivative dir = flow name - docs.md — if exists, update collection paths

5. CLAUDE.md files

  • CLAUDE.md (projio root) — remove pipe from tool listings
  • packages/pipeio/CLAUDE.md — remove pipe references, update tool descriptions

6. Lifecycle module (packages/pipeio/src/pipeio/notebook/lifecycle.py)

Update nb_lab() and nb_audit() — these use pipe/flow for grouping. Change to flow-only.

Constraints

  • Run both pipeio tests and projio tests
  • Save with datalad_save (recursive)

Acceptance Criteria

  • [ ] docs_collect() produces docs/pipelines/{flow}/ structure (with mods/ and scripts/ subdirs)
  • [ ] Modkey citekeys use {flow}_mod-{mod} format
  • [ ] Agent instructions reference flow-only addressing everywhere
  • [ ] No mention of "pipe" as an addressing concept in any spec or CLAUDE.md
  • [ ] All tests pass

Result

(Filled in after execution)

Batch Result

  • status: failed
  • batch queue_id: 48c064cff89c
  • batch duration: 1800.1s