ResearchTools — Manual

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ResearchTools is an AI-assisted toolbox for researcher-professors and graduate students
who want to design, find and fix the issues hiding in their academic design and writing
before a reviewer, a thesis committee, or a grant panel does. On the software side,
in code, PCB, and 3D CAD design. Full pitch, the 2026 roadmap, and this manual's own
conventions: docs/manual/00-purpose.md.

Never let an LLM do your work for you. Use it to improve your work, find your weaknesses,
and help you improve yourself. Never use these tools to conduct a formal or professional
assessment, and do not let the tool make decisions for you. Use at your own risk.

This file is the entry point only. The manual is split into chapters under docs/manual/,
the same way Architecture.md is already split into layers instead of kept
as one flat file — this keeps each topic at a readable size instead of one 1300-line page.

See it in action

The rt-observe dashboard watching a live session: hook flow, fan-out to the two memories
(Obsidian vault, graphify graph), and a spawned subagent, all on loopback with no external
service. Full walkthrough: docs/manual/07-rt-observe-dashboard.md.

Quickstart

git clone https://github.com/LARi-UQAC/ResearchTools.git
cd ResearchTools
.\setup.ps1 -All -Personal   # config + Claude links + all tool mirrors
.\setup.ps1 -InstallPython   # optional: creates .venv-skills for the offline test suite

Full install steps (junctions, other-tool mirrors, prerequisites table):
docs/manual/01-installation.md.

The two memories

Two memories back this toolkit, and neither is read or written directly: the Obsidian vault
(what was learned, across every project) and the graphify code graph in graphify-out/
(what this repository's code IS right now). Both are reached only by dispatching the
local-writer agent. The graph's own state is read-only via
scripts/audit/check-graph-health.ps1. Full design:
docs/manual/04-skills.md.

Manual chapters

At a glance — commands drive agents, agents draw on skills, and both memories are reached
only through local-writer (detail: 04-skills.md):

graph LR
  U["You"] -->|"/command"| CC["Your Harness"]
  CC --> AG["Agents"]
  AG --> SK["Skills"]
  SK --> EXT[("Scopus / Gemini /<br/>Copilot APIs" / etc.)]
  AG -->|"dispatch local-writer"| VAULT[("Obsidian vault<br/>what was learned")]
  AG -->|"dispatch local-writer"| GRAPH[("graphify graph<br/>what the code is")]

Relationship diagrams and the 7-layer execution architecture for this repository:
Architecture.md. The architecture shared with the sibling repository
ThesisTracker (form catalogue, twenty-unit delivery plan) is a separate file,
NEW_ARCHITECTURE.md — see chapter 09 above; do not confuse the two.