research

Personal research plugin for Claude Code. Keeps a central, searchable, lifecycle-managed knowledge base of everything you research — with project-local symlinks so research stays visible alongside code.

Install

/plugin marketplace add tyroneross/research-plugin
/plugin install research@research-plugin

Then install the Python dependency:

pip install pyyaml            # required
pip install sympy             # optional (v0.2 symbolic verification)

Restart Claude Code. The /research:* slash commands should autocomplete; the research skill activates on phrases like "research X", "investigate Y", "what's the current state of Z".

First run

By default, any /research ... session writes its markdown corpus to ~/dev/research/ and keeps its SQLite index there too. Or bootstrap explicitly:

python ~/.claude/plugins/research/research.py init

Roots

The plugin now supports separate roots for content and derived index/state:

• RESEARCH_CONTENT_DIR — canonical markdown corpus, generated markdown views, archive, inbox, project symlinks
• RESEARCH_INDEX_DIR — SQLite DB, linked-project registry, verifier logs, extract cache
• RESEARCH_BASE_DIR — legacy compatibility alias; if the new vars are unset, both roots fall back here

Default behavior:

• content root: ~/dev/research/
• index root: ~/dev/research/

Layout

Content root:

• <content-root>/topics/<topic-tree>/<slug>.md — canonical entries
• <content-root>/indices/<topic>.md — auto-generated Maps of Content
• <content-root>/index.md, by-topic.md, by-project.md, review-due.md, PORTFOLIO.md — auto-generated dashboards
• <content-root>/archive/ — archived entries (never deleted, redirect stubs left behind)
• <content-root>/inbox/ — fleeting notes / files queued via /research:ingest --inbox
• <content-root>/projects/ — project symlink views

Index root:

• <index-root>/.db.sqlite3 — FTS5 index, domain scores, verifier state
• <index-root>/.linked-projects.json — linked external project registry
• <index-root>/verifier-log/ — verification artifacts
• <index-root>/.extract-cache/ — Omniparse extract cache

Per-project research

Two mechanisms, depending on who authored the research.

Plugin-authored entries — when an entry's frontmatter includes projects: [foo] and a project directory exists, /research:save maintains a symlink at <content-root>/projects/foo/<slug>.md pointing to the canonical entry under <content-root>/topics/. The project directory is not modified. Pass --with-project-index if you also want a <project>/RossLabs-Research.md index file written into the project (opt-in).

Pre-existing project research — for directories like ~/dev/git-folder/SpeakSavvy-iOS/docs/research/ that predate this plugin and should not be restructured, use /research:link-project <name> <path>. The plugin walks the directory recursively for *.md files, extracts a title and a 1-line summary from each, records the registration in <index-root>/.linked-projects.json, and creates symlinks at <content-root>/projects/<name>/<filename>. The source directory is never modified.

Both mechanisms surface in <content-root>/PORTFOLIO.md under separate sections ("Plugin-managed projects" and "Linked external research directories"). /research:index refreshes both.

Legacy v0.3.0 artifacts (<project>/research/ file copies, <project>/research/.live/ symlinks, <project>/RossLabs-Research.md) are preserved as-is — v0.3.1 does not write to these paths by default, but also does not delete them. A one-time note is printed when the plugin touches a project that still has them.

Subcommands

Command	Purpose
/research:init	Bootstrap the configured content and index roots
/research:save <file>	Persist an entry (Phase 6 entry point); writes canonical + project symlink, regenerates portfolio. --with-project-index to also write <project>/RossLabs-Research.md
/research:ingest <path>	Bulk-ingest existing markdown files; --inbox to park, --save to persist drafts
/research:search <query>	FTS5-ranked search
/research:list [N]	Recent entries
/research:link <slug>	Retroactive project symlink for a saved entry
/research:link-project <name> <path>	Register an existing external research directory (plugin does not modify it)
/research:sync	Rebuild SQLite from canonical topic markdown; use --prune-missing after moves or migrations
/research:index	Rebuild central indexes, refresh plugin-managed symlinks, re-scan linked external projects, and rewrite PORTFOLIO.md
/research:recategorize	Suggest splits for top-level topics that have grown too large (read-only)
/research:archive <slug>	Move to archive, leave redirect stub
/research:score <url>	Inspect or set source tier for a domain
/research:verify <slug>	Run claim verification on an entry
/research:table-profile <path>	Profile CSV/TSV/JSON data before quantitative analysis
/research:db-profile <path>	Profile a SQLite database schema, row counts, indexes, and foreign keys
/research:analyze-plan --input <path> --question "..."	Generate a self-contained stdlib Python analysis plan/script
/research:analyze-run --plan <analysis-plan.yaml>	Run the generated analysis script and write results/audit artifacts
/research:review	Surface stale / review-due entries
/research:compress <slug>	Compact an entry's TL;DR and Raw sections
/research:extract <path>	Route PDF/Excel/PPTX/Python/dir through vendored Omniparse

Vendored dependencies

/research:extract routes document parsing (PDF, Excel, PPTX, Python, directories) through a self-contained, pre-built copy of @tyroneross/omniparse that ships with this plugin at vendor/omniparse/. All JS runtime deps are inlined — no npm install needed. Only node >= 18 must be on PATH.

• Upstream: https://github.com/tyroneross/Omniparse (see vendor/omniparse/.upstream for the exact commit)
• License: FSL-1.1-MIT (copied verbatim to vendor/omniparse/LICENSE)
• Re-vendor: follow vendor/omniparse/BUILD.md

A user-installed omniparse on PATH will be preferred over the vendored copy when present.

Philosophy

• Non-LLM parsers first, LLM for judgment — Claude's WebFetch/Read extract content; scripts compute what can be computed.
• Code does the math — quantitative/database claims should go through profile → analysis plan → generated stdlib Python script → results/audit with High/Medium/Low certainty.
• Deterministic over clever — same URL always scores the same tier; same claim always routes to the same verifier.
• Never delete — archive + redirect stubs preserve all inbound links.
• Three layers — TL;DR (≤150 words, extractive), Notes (bolded key passages + citations), Raw (verbatim source excerpts for future verification).

Codex

This package now ships an additive Codex plugin surface alongside the existing Claude Code package. The Claude package remains authoritative for Claude behavior; the Codex package adds a parallel .codex-plugin/plugin.json install surface without changing the Claude runtime.

Package root for Codex installs:

• the repository root (.)

Primary Codex surface:

• skills from ./skills when present
• MCP config from (none) when present

Install the package from this package root using your current Codex plugin install flow. The Codex package is additive only: Claude-specific hooks, slash commands, and agent wiring remain unchanged for Claude Code.