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Ecosystem

projio is the workspace and orchestration layer for a small documentation and knowledge-tool ecosystem.

The split is deliberate:

  • projio owns project-local scaffolding, docs-site workflows, and MCP exposure
  • indexio owns semantic search and chat-backed retrieval
  • biblio owns bibliography ingestion, enrichment, and bibliography-first sites
  • notio owns notes, structured project logs, and manuscript assembly — including the result note type for individual scientific findings
  • codio owns code-library and code-context discovery
  • pipeio owns pipeline authoring, contracts, notebook lifecycle, and Snakemake integration — engineering, not science
  • figio owns declarative figure orchestration — FigureSpec YAML to SVG/PDF composition
  • questio owns research questions, hypothesis tracking, prior art, and the binding between questions and results/deliverables

The engineering-vs-science boundary between pipeio and questio/notio/deliverables is documented in delegation-model.md — read that next if you're authoring a new flow, result, or report and wondering where the content should live.

Role diagram

flowchart TD
    U[Project repository] --> P[projio]

    P --> S[Scaffolding and repo conventions]
    P --> D[Site workflows and deployment glue]
    P --> M[MCP server and tool surface]

    M --> I[indexio]
    M --> B[biblio]
    M --> N[notio]
    M --> C[codio]
    M --> Pi[pipeio]
    M --> F[figio]

    I --> IR[Semantic search and chatbot retrieval]
    B --> BR[Bibliography workspace and publication]
    N --> NR[Notes, logs, manuscripts, and project memory]
    C --> CR[Code discovery and reuse intelligence]
    Pi --> PiR[Pipeline authoring, contracts, notebooks]
    F --> FR[Declarative figure orchestration]

    B -. registers sources .-> I
    N -. registers sources .-> I
    C -. registers sources .-> I
    Pi -. notebooks .-> N
    F -. panels .-> N

projio is the coordinator. The sibling packages stay focused on their own domain, and indexio acts as shared retrieval infrastructure where cross-package search is needed.

GitHub Pages

Mental model

Use projio when you need a repo-wide entrypoint that ties those tools together. Use the tool-specific docs when you are working inside one subsystem in depth.