Implement pipeio flow rename with modkey.bib citekey update

Goal

Add a pipeio flow rename CLI command and pipeio_flow_rename MCP tool that safely renames a flow within a pipe, updating all pipeio-managed references. Preview-first (dry run by default, --yes to execute).

Scope: flow rename only. Pipe rename is excluded — derivative directories are tied to pipe names via datalad subdatasets, making pipe rename risky and requiring datalad-level coordination.

Context

Flow names appear in multiple pipeio-managed entities. A rename must update all of them atomically or provide a clear rollback. The modkey.bib citekeys use the pattern pipe-{pipe}_flow-{flow}_mod-{mod} and are referenced in manuscripts via pandoc-citeproc ([@pipe-X_flow-Y_mod-Z]).

Entities affected by flow rename

Entity	Location	What changes
Registry	.projio/pipeio/registry.yml	Key pipe/old_flow → pipe/new_flow, .name field, code_path, config_path, doc_path
Code directory	code/pipelines/{pipe}/{old_flow}/	mv to {new_flow}/
Docs tree	docs/pipelines/{pipe}/{old_flow}/	mv to {new_flow}/
modkey.bib	docs/pipelines/modkey.bib	All citekeys containing flow-{old_flow} → flow-{new_flow}, plus title and note fields
Manuscript/note references	*.md, *.tex files	[@pipe-X_flow-old_mod-Z] → [@pipe-X_flow-new_mod-Z]
MkDocs nav fragment	Generated by pipeio docs nav	Regenerate after rename
notebook.yml	{flow}/notebooks/notebook.yml	No change (no flow name embedded)
Snakefile	{flow}/Snakefile	No change (no flow name embedded)
Flow config	{flow}/config.yml	No change (no flow name embedded)

What does NOT change

• Pipe name (excluded from scope)
• Mod names within the flow
• Notebook paths within notebook.yml (relative to flow root)
• Snakefile rule names
• Flow config content

Design

CLI

pipeio flow rename <pipe> <old_flow> <new_flow>          # dry-run preview
pipeio flow rename <pipe> <old_flow> <new_flow> --yes    # execute

MCP tool

pipeio_flow_rename(pipe: str, old_flow: str, new_flow: str, execute: bool = False) -> dict

Returns a plan with all changes that will be made. When execute=False (default), nothing is modified — just the preview. When execute=True, applies all changes.

Implementation steps (inside the tool)

1. Validate — old flow exists in registry, new flow name doesn't conflict
2. Build plan — list all file moves, registry edits, bib rewrites, citekey replacements
3. If execute: a. Move code directory b. Move docs directory c. Update registry.yml (rewrite key, name, all paths) d. Rewrite modkey.bib (string replace on citekeys, titles, notes) e. Grep-and-replace citekey references in docs/ and notes/ markdown files f. Regenerate MkDocs nav fragment
4. Return — plan + status (previewed | executed | error)

Citekey replacement

Pattern: pipe-{pipe}_flow-{old}_mod-{mod} → pipe-{pipe}_flow-{new}_mod-{mod}

This is a simple string replacement since the flow segment is delimited by _flow- prefix and _mod- suffix. Apply to: - modkey.bib (citekeys, title fields, note fields) - All .md files under docs/ and notes/ (pandoc citations [@citekey]) - All .tex files if any

Files to implement in

• packages/pipeio/src/pipeio/rename.py — new module with flow_rename(root, pipe, old, new, execute)
• packages/pipeio/src/pipeio/mcp.py — mcp_flow_rename() wrapper
• packages/pipeio/src/pipeio/cli.py — pipeio flow rename subcommand
• src/projio/mcp/pipeio.py — pipeio_flow_rename() wrapper
• src/projio/mcp/server.py — tool registration

Acceptance Criteria

• [ ] pipeio flow rename pipe old new shows preview of all changes
• [ ] pipeio flow rename pipe old new --yes executes rename
• [ ] Registry.yml updated with new flow name and paths
• [ ] Code directory moved
• [ ] Docs directory moved
• [ ] modkey.bib citekeys updated
• [ ] Pandoc citation references updated in docs/*.md
• [ ] MkDocs nav regenerated
• [ ] MCP tool pipeio_flow_rename works with execute=False (preview) and execute=True
• [ ] All existing tests still pass

Result

(Filled in after execution)