research-buddy 1.19.0

Structured AI research collaborator — generates high-fidelity HTML from versioned JSON or Markdown research documents.

Research Buddy v1.19.0

A structured AI research collaborator for any domain.

Format: v2 Markdown (recommended) and v1 JSON (legacy)

v2 Markdown is the recommended format for new projects as of 1.5. v1 JSON remains supported for existing projects but is on a deprecation path; new features land on v2 first.

• v2 Markdown (default for new work): YAML frontmatter + Markdown body with HTML-comment anchors (<!-- @anchor: ... -->, <!-- @rule: ... -->, <!-- @da: ... -->). Source of truth = *_v*-source.md (agent-edited, full framework). The reader-facing artifact is the clean view *_v*.md (framework stripped) or the rendered HTML. Each top-level ## H2 becomes a tab.
• v1 JSON (legacy): structured JSON with rich block types (callouts, verdicts, fixed-width tables). Source of truth = *_v*.json. Continue using for projects already on v1; migrate to v2 with research-buddy migrate-v1-to-v2.

build, validate, and upgrade dispatch on file extension. migrate-v1-to-v2 and clean operate on v2 only.

How it works

The AI agent reads the framework embedded in your research document and behaves as a Research Buddy for the full lifetime of the project. Every session produces an updated, versioned source file — the source of truth — and a rendered HTML document for reading.

Session zero (v2 Markdown flow — recommended): run research-buddy init my-project/ to scaffold source/research-document.md. Upload that file to an AI assistant. The agent introduces itself, asks questions to understand the project, does discovery research, and proposes the initial structure — sections, source tiers, queue items, and methodology rules tailored to your domain. Output: {file_name}_v1.0-source.md. Run research-buddy build my-project/source/{file_name}_v1.0-source.md to generate HTML.

Subsequent sessions: upload the latest *-source.md, say "Continue research" — the agent picks up exactly where you left off and works through the queue one topic at a time in exactly 2 turns.

The two-turn protocol (research turn + vet/write turn) applies to both formats. Legacy v1 JSON flow: use research-buddy init my-project/ --v1; the agent produces versioned .json files instead of .md sources.

Install

For users (pip)

pip install research-buddy

PDF export is an optional extra (weasyprint is a large install with system-level dependencies, so it's not pulled in by default):

pip install "research-buddy[pdf]"

For development

uv sync --extra dev
# or:
pip install -e ".[dev]"

For AI Agents or AI users

If you are an AI agent or a user of a chatbot looking for the initial research template (v2 Markdown, recommended):

• Direct download: starter.md
• Package path: research_buddy.starter.md (when installed via pip)
• Source path: src/research_buddy/starter.md (in this repository)

Download this file and attach it into an AI chatbot session to start researching. The AI agent will know what to do.

For the legacy v1 JSON template:

• Direct download: starter.json
• Package path: research_buddy.starter.json (when installed via pip)
• Source path: src/research_buddy/starter.json (in this repository)

Generating HTML

After each research session, to give the user a readable HTML document:

pip install research-buddy
research-buddy build my-project/source/my-project_v1.0-source.md

The output will be [file_name].html in the project directory.

Workflow

1. Session start: User uploads their *-source.md file (v2) or .json file (v1 legacy). If new, ask them to run research-buddy init <project-name> first to get the starter template.
2. Session end: After making changes, run research-buddy build <source-file> to generate HTML. Tell the user the HTML is ready and they can download it.
3. Next session: Ask the user to upload the latest *-source.md (v2) or .json (v1) file and say "Continue research".

The source file is always the source of truth — never the HTML.

Quick start

# Scaffold a new project — v2 Markdown by default
research-buddy init my-project/

# Upload my-project/source/research-document.md to your AI assistant
# The agent runs session_zero and produces {file_name}_v1.0-source.md

# Build HTML from the versioned output
research-buddy build my-project/source/my-project_v1.0-source.md

# Or point at the project directory — it finds the latest version automatically
research-buddy build my-project/

# Open the result
open my-project.html

For an existing v1 JSON project, pass --v1 to init and use the v1 flow (versioned .json files, --watch/--pdf available on build).

Research protocol

Every session follows a strict, high-integrity 2-turn workflow:

1. Turn 1: Research & Brief
   • Agent reads the in-document framework, detects session state, and emits a second-opinion brief before touching any research tool. (research-buddy turn1 <file> pre-fills the brief from frontmatter + the top queue row.)
   • Agent performs discovery research using domain-appropriate Tier 1 sources with inline citations, then STOPS and waits for the user to provide results from other researchers (other AI agents, human experts, etc.).
2. Turn 2: Vet & Write
   • User submits findings from other researchers.
   • Agent vets each finding, resolves pre-registered hypotheses, then performs an atomic write to the versioned source file — *_vX.Y-source.md for v2 Markdown (recommended), or *_vX.Y.json for v1 legacy — bumping the version.
   • User runs research-buddy build <source-file> to generate HTML.
   • New research topics are queued for the next session, not shoehorned into the current one.

Failure modes are explicit: the in-document framework lists failure modes that agents use to self-check before and after every action.

File naming

The tool uses the file_name field from your document to name outputs.

v2 Markdown (recommended)

File	Purpose
source/research-document.md	Unversioned starter — uploaded to the agent for session zero
[file_name]_v1.0-source.md	First versioned source, produced by session zero
[file_name]_v1.1-source.md	After first research session
[file_name]_vX.Y.md	Clean view (framework stripped) — shareable artifact
[file_name]_vX.Y.html	Versioned HTML build
[file_name].html	Latest stable HTML build

v1 JSON (legacy)

File	Purpose
source/research-document.json	Unversioned template — never modified after init
[file_name]_v1.0.json	First project file, produced by session zero
[file_name]_v1.1.json	After first research session
[file_name]_vX.Y.html	Versioned HTML build
[file_name].html	Latest stable HTML build

Batch Processing (v1 JSON only)

You can process multiple v1 JSON files in order. This is useful for replaying the full version history of a legacy project:

# Processes files in the given order. The final [file_name].html 
# will be generated from the last file in the list.
research-buddy build v1.0.json v1.1.json v1.2.json

Commands

research-buddy init <dir>

Scaffold a new project. Defaults to the recommended v2 Markdown form: creates source/research-document.md (the bundled v2 starter, frontmatter patched with --title/--subtitle if provided) and versions/. Pass --v1 to scaffold a legacy v1 JSON project instead (source/research-document.json).

research-buddy init my-project/ [--title "Project Name"] [--subtitle "..."]
research-buddy init legacy-project/ --v1 --title "..."   # legacy JSON

research-buddy build <path...>

Build HTML from document JSON(s) or Markdown file(s). Accepts files, directories, or both. Dispatches on file extension: .json → v1 pipeline, .md → v2 pipeline (same single-file chrome — tab bar, sidebar nav, theme toggle, hljs).

research-buddy build my-project/                    # latest version in source/
research-buddy build my-research_v1.5.json          # v1 JSON
research-buddy build my-research_v1.0-source.md     # v2 Markdown
research-buddy build a.json b.json                  # batch JSON IN ORDER
research-buddy build my-project/ --watch            # rebuild on change (.json only)
research-buddy build my-project/ --pdf              # + PDF (v1 only, requires weasyprint)
research-buddy build my-project/ --output master.html
research-buddy build my-project/ --validate-only    # v1 only

Mixing .json and .md inputs in a single invocation is rejected; --watch and --pdf are not yet supported for .md inputs. The MD build strips the framework block by default (matches the JSON build's "reader-facing" semantics — the framework is for the agent reading the source, not for HTML readers).

research-buddy validate <path...>

Validate JSON or Markdown documents. Dispatches on extension: .md → v2 mechanical validator (frontmatter, anchor pairing, link resolution, ID uniqueness); everything else → v1 JSON validator (schema + reference ordering + version compat).

research-buddy validate my-research_v1.0-source.md
research-buddy validate my-research_v1.1-source.md --prior my-research_v1.0-source.md

The optional --prior flag (v2 only) compares against an earlier version of the same file and enforces append-only invariants: anchors, Discarded Alternatives, References, and Changelog entries must never disappear.

research-buddy clean <path...> (v2)

Generate the shareable clean view from a v2 source file: strips the framework block (<!-- @anchor: framework.core --> … <!-- @end: framework.reference -->) and regenerates the title block from the YAML frontmatter. Output: {file_name}_v{version}.md alongside the source.

research-buddy clean my-research_v1.0-source.md
research-buddy clean my-research_v1.0-source.md -o /tmp/out.md

Refuses to run on a starter file (project.domain is null in the frontmatter) — there's nothing to clean until session zero fills in the project specification.

research-buddy migrate-v1-to-v2 <path...> (v2)

One-way migration from a v1 JSON document to a v2 Markdown source file. Maps meta.* + agent_guidelines.project_specific.* to YAML frontmatter; replaces the old framework with the v2 framework block copied from the bundled starter.md; promotes research-tab sections to top-level H2s; converts verdict blocks to @rule / @da blocks with stable IDs.

research-buddy migrate-v1-to-v2 my-research_v3.0.json     # writes my-research_v3.0-source.md
research-buddy migrate-v1-to-v2 old.json -o new-source.md
research-buddy migrate-v1-to-v2 old.json --force          # overwrite existing output

Refuses to overwrite an existing output unless --force is passed. After migration, run research-buddy validate <output>.md to confirm the result.

research-buddy upgrade <path...>

Re-sync a project source against the installed starter template. Dispatches on file extension:

• .json → v1 path. Replaces agent_guidelines.framework and agent_guidelines.session_protocol wholesale, preserves session_zero.note so initialized projects do not re-run session zero, leaves agent_guidelines.project_specific untouched, and bumps meta.research_buddy_version. Appends a dated entry to meta.format_note only when something actually changed.
• .md → v2 path. Replaces the framework block (everything between <!-- @anchor: framework.core --> and <!-- @end: framework.reference -->) with the installed starter.md's block, preserves all project-owned content (frontmatter values, project specification, queue, tracker, rules, DAs, sessions, journey, references, changelog), bumps research_buddy_version, renames legacy format_version → doc_format_version, and inserts missing project.source_tiers / project.domain_rules frontmatter fields with null values.

research-buddy upgrade my-project/                                     # v1 dry-run
research-buddy upgrade my-project/ --apply                             # v1 write + validate
research-buddy upgrade my-project/source/foo_v1.0-source.md            # v2 dry-run
research-buddy upgrade my-project/source/foo_v1.0-source.md --apply    # v2 write + validate
research-buddy upgrade ... --apply --no-validate                       # skip post-write validation

Exit codes: 0 clean (no changes or applied), 1 dry-run found changes, 2 error (bad path, validation failed, starter missing, malformed framework block).

Project layout

my-project/
├── source/
│   └── research-document.json    # Template (agent uploads this for session_zero)
├── versions/                     # Versioned HTML builds
│   └── v1.0.html
├── [file_name].html              # Latest stable build (copy of most recent version)
└── theme.css                     # Optional CSS overrides

Multi-language support

The document language is set in session_zero based on the user's preference and recorded in frontmatter. language accepts a string ("Spanish") or an object ({code: es, label: Español}). It drives two things:

• The HTML lang attribute (set automatically).

• Localized section headings (v2 HTML). The framework names its user-facing sections in English ("Open Research Queue", "References", …) because their slugs are load-bearing cross-link targets — translating them in the source would break every [Queue](#open-research-queue) link. So when language.code is a shipped language (currently Spanish), the HTML build displays those headings in that language while keeping the English slugs/ids, so nothing breaks. Add or override labels — and enable languages not shipped built-in — with an optional section_labels: frontmatter mapping (English heading → label):

  section_labels:
    Open Research Queue: Cola de tareas
  

  Localization is HTML-render-only; the clean-view Markdown keeps English headings (there a heading's slug is its text, so display and link target can't diverge). The framework prose itself stays English and is stripped from the clean view / HTML.

Research content (findings, decisions, status text) is authored in the document language by the agent. The legacy v1 meta.ui_strings field is carried forward on migration but is not rendered in v2 — there is no fixed status column, so the agent writes status text (and rb-ok/rb-flag chips) directly in the document language.

Document format (v1 JSON)

This section applies to the legacy v1 JSON format. v2 Markdown documents use standard Markdown + YAML frontmatter; see src/research_buddy/starter.md for the canonical v2 structure.

The v1 JSON schema is bundled with the package. For reference, see src/research_buddy/schema.json in the repository, or the matching path inside the installed wheel (research_buddy/schema.json).

Block types (v1 JSON)

Type	Key fields
p	md
h3, h4	md, id, badge
code	text, lang
callout	md, variant (blue|green|amber|red|purple), title
verdict	badge (adopt|reject|defer|pending), label, md
table	headers[], rows[][]
ul, ol	items[]
card_grid	cols (2|3), cards[{title, md}]
phase_cards	cards[{phase, title, items[]}]
usage_banner	title, items[]
references	items[{version, date, text}]
svg	html (raw SVG string)

Schema compatibility (v1 JSON)

meta.research_buddy_version is required in all v1 documents. The validator warns if it is missing. When this version changes, schema or build script behaviour may change — always use the template that matches your installed version.

Version compatibility (tool ↔ document)

Research Buddy uses MAJOR.MINOR.PATCH semver. Both formats record the tool version that produced them:

• v2 Markdown: research_buddy_version in YAML frontmatter.
• v1 JSON (legacy): meta.research_buddy_version.

v1 JSON: active version check

Every research-buddy build and research-buddy validate on a v1 JSON document actively compares the installed CLI version against the version in the document:

Comparison	Severity	What happens
Exact match	silent	Nothing to worry about.
Only PATCH differs (e.g. 1.0.3 vs 1.0)	silent	Patches are strictly backwards-compatible. Treated as equivalent.
Tool MINOR newer than doc (same MAJOR)	silent	No action required. Doc is fully compatible. The agent bumps meta.research_buddy_version on the next write.
Tool MINOR older than doc (same MAJOR)	warning	Doc may use features your tool does not render correctly. Run pip install --upgrade research-buddy.
MAJOR differs	error	Schema is not guaranteed to match. Either install the matching major (pip install 'research-buddy==1.*') or start an AI session and say "Migrate to research-buddy vX.Y" so the agent updates the document structure.

Algorithmic rule: the validator compares MAJOR.MINOR only. Patch-level differences are ignored — 1.0.3 and 1.0 behave the same.

v2 Markdown: agent-managed version

In v2 Markdown, research_buddy_version is checked only for presence (the field is required). No active MAJOR/MINOR comparison gate exists. The agent updates the field to the current tool version on each Turn 2 atomic write, so it stays in sync automatically. Run research-buddy upgrade <file>.md --apply to refresh the framework block and frontmatter when you upgrade the CLI.

What if my document is on an older version?

If you're upgrading the CLI to a newer minor (e.g. tool 1.1.0, doc 1.0.3) there is nothing to do: your build continues to produce HTML as before.

If you're moving across a major boundary, the CLI (for v1 documents) will tell you, point at CHANGELOG.md, and give you a copy-pasteable command to pin the matching major (if you want to keep your current doc as-is) or an instruction to hand to the agent (if you want to migrate).

Development

make sync           # Install dev dependencies
make lint           # ruff + mypy
make format         # Auto-fix + format
make test           # Run full test suite
make update-skills  # Pull latest shared Claude skills

Examples

The starter-example/ directory contains pre-built HTML outputs from the bundled starters:

• starter.html — built from starter.json (v1 JSON pipeline).
• starter-md.html — built from starter.md (v2 Markdown pipeline, framework stripped to match the v1 reader view).

Regenerate with:

make regen-example      # v1 only
make regen-md-example   # v2 only
make regen-examples     # both

License

MIT