Agent-native research workspace. A deterministic CLI that ingests arXiv / PDF / LaTeX / Zotero papers into an Obsidian-compatible knowledge graph, with local hybrid search (BM25 + vectors), claim-level provenance, and a nightly literature radar.
Skill Claude CodeCodex
Answer MAGI usage and troubleshooting questions from the installed manual: look up the exact error in magi guide --symptoms/--search, read the relevant chapter, verify the workspace state, and hand back the exact fix command. Use whenever a magi command errors or the user asks how to install, migrate, ingest, build…
Skill Claude CodeCodex
Triage literature-radar digests: score each candidate paper against the local wiki, file bd survey issues for keepers, and queue selected PDFs for ingestion.
Skill Claude CodeCodex
Chat with the knowledge base. Answers user questions by dynamically employing RAG context extraction, graph database queries, and targeted keyword searches to provide cited, hallucination-free answers.
Skill Claude CodeCodex
Audit the compiled wiki pages to cross-check statements, highlight scientific contradictions, and output theses using a Map-Reduce architecture.
Skill Claude CodeCodex
Compile raw sources into detailed, Obsidian-compatible, interlinked Markdown pages under wiki/ references/ and concepts/.
Skill Claude CodeCodex
Deduplicates concepts, splits overly broad concepts, and synthesizes multi-source concept definitions by dynamically searching and analyzing all papers that reference them.
Skill Claude CodeCodex
Write paper drafts inside the workspace: drafts/ convention, evidence-backed writing with magi search, citation export with magi bib, and LaTeX export.
Skill Claude CodeCodex
Act as a Concept Miner to inspect compiled papers, check concept linkage density, and spawn subagents to extract missing mathematical and physical concepts.
Skill Claude CodeCodex
Extract Obsidian-style relationships (wikilinks, tags, aliases) into a structured AI-friendly SQLite graph database.
Skill Claude CodeCodex
Initialize a central Hub directory for managing multiple topic wikis.
Skill Claude CodeCodex
Manage topics in the central Hub: route slugs to paths, list topics, and archive or restore topics.
Skill Claude CodeCodex
Put papers into a knowledge base from whatever the user has — an arXiv link, a journal page, a DOI, a citation, or a screenshot. Identifies each one, queues it, runs the deterministic ingest pipeline, and hands the batch back for approval.
Skill Claude CodeCodex
Ingest new academic papers, notes, or web articles into the raw/ folder of your active topic wiki.
Skill Claude CodeCodex
Ingest new academic papers or PDFs into the raw/ folder of your active topic wiki using the local OCR model configured in config.yaml.
Skill Claude CodeCodex
Initialize a new topic workspace folder with standard raw/, wiki/, inbox/, and output/ directories.
Skill Claude CodeCodex
Statically check and repair double-bracket linkages and frontmatter within your compiled wiki directory.
Skill Claude CodeCodex
Works through every malformed LaTeX formula in the workspace one at a time — the OCR and PDF-conversion damage that magi math format cannot fix mechanically.
Skill Claude CodeCodex
Spawn parallel academic subagents to perform multi-perspective research on a given query and compile a detailed synthesis report.
Skill Claude CodeCodex
Automatically builds semantic links between concept markdown files by calculating vector similarity using a local Ollama embedding model.
Skill Claude CodeCodex
Deduplicates, normalizes, and reduces sprawling tags and aliases across the knowledge graph using a Map-Reduce architecture.