Skip to content

title: "MCP tools missing for index setup and source registration status: done created: 2026-03-26 updated: 2026-03-26 timestamp: 20260326-174001-720656 tags: [issue] source: agent-observation project_primary: projio capture_id: 20260326-173959-e28c29 confidence: 1.0 status: done transcript_file: /storage2/arash/worklog/workflow/captures/20260326-173959-e28c29/transcript.txt

MCP tools missing for index setup and source registration

Problem

The MCP layer covers querying well (rag_query, rag_query_multi, codio_discover, codio_list) but not setup/registration. An agent cannot bootstrap or manage a project's search index without dropping to CLI (biblio rag sync, codio rag sync). This breaks the MCP-first workflow — agents hit a wall when they need to set up indexing for the first time or register new sources.

Discovered during pixecog plan audit: indexio_build ran but only indexed docs because biblio and codio sources weren't registered (no MCP tools to do so).

Missing MCP tools

indexio

  • indexio_sources_list — List currently registered sources with stats (corpus, glob, chunk count). Lets an agent inspect what's indexed before querying.
  • indexio_sources_sync — Meta-sync that triggers all subsystem syncs (biblio, codio) in one call. Alternatively, let each subsystem own its sync tool and have this as a convenience wrapper.

biblio

  • biblio_rag_sync — Register biblio's docling sources into the indexio config. Wraps the existing biblio rag sync CLI. After this, indexio_build --sources biblio_docling picks them up.

codio

  • codio_rag_sync — Register codio library sources into the indexio config. Wraps the existing codio rag sync CLI. Generates codio-notes, codio-catalog, and per-library codio-src-{name} sources from the registry.
  • codio_add — Register a library into the codio registry with metadata (kind, storage, capabilities, path). Currently the only way to populate the registry is CLI or manual YAML editing. An agent that discovers a useful library (e.g. via codio_discover returning empty) has no way to register it.

Expected workflow after fix

agent: codio_add(name="yasa", kind="external_mirror", storage="attached", path="/storage/share/codelib/raphaelvallat--yasa")
agent: codio_rag_sync()          # registers codio-src-yasa into indexio config
agent: biblio_rag_sync()         # registers biblio_docling into indexio config
agent: indexio_build()           # builds full index across docs + biblio + codelib
agent: rag_query("spindle detection", corpus="codelib")  # now works

Implementation notes

  • The sync functions already exist: biblio.rag.sync_biblio_rag_config() and codio.rag.sync_codio_rag_sources() — just need MCP wrappers
  • codio_add needs a new function but the registry schema is defined
  • indexio_sources_list can read from the config + the status manifest that indexio_build writes
  • Consider whether indexio_build should auto-trigger syncs before building (so agents don't need to remember the sync step)

Source context: pixecog

PixEcog (pixecog): Neuropixels and ECoG dataset and analysis

Recent commits: 

6429574 untrack
614785c remove CI builds/ from tracking, add to gitignore
63f0884 pipeio notebook test

README:

type: readme

Quick Start for Collaborators

Follow this checklist to get started with Pixecog documentation and workflows.

🐀 Pixecog Project — Compact Overview

Core principles

  • One immutable BIDS raw dataset (raw/) as the canonical baseline
  • Each analysis pipeline ha