+
+- :material-laptop:{ .lg .middle } __As a local dev tool__
+
+ ---
+
+ Install the Docker shim, then `init` and `scan` your repos and wire your editor - no Python or
+ Node on the host. This is the default install.
+
+ [:octicons-arrow-right-24: Run with Docker](docker.md)
+
+- :material-server-network:{ .lg .middle } __As a service__
+
+ ---
+
+ A containerized `whygraph-mcp` endpoint that real applications - not just editors - connect to
+ for git-based analysis of a target repo.
+
+ [:octicons-arrow-right-24: WhyGraph as a service](service.md)
+
+
+
+Most people start with the local tool. Reach for the service model when you're building an
+application that needs the *why* behind code - a review bot, an onboarding assistant, an internal
+portal.
diff --git a/docs/deploy/service.md b/docs/deploy/service.md
new file mode 100644
index 0000000..cae7107
--- /dev/null
+++ b/docs/deploy/service.md
@@ -0,0 +1,89 @@
+# WhyGraph as a service
+
+Editors aren't the only thing that can talk to WhyGraph. The MCP server is a plain stdio program, so
+any application that speaks MCP can connect to it for git-based analysis of a target repo. Think of a
+review bot, an onboarding assistant, or an internal dev portal that needs the *why* behind a chunk of
+code - not just the code.
+
+This page covers that model: a containerized `whygraph-mcp` endpoint a third-party app drives over
+MCP, reading the same on-disk data your scan produces.
+
+## The shape of it
+
+A consuming app launches the WhyGraph image, mounts the target repo at `/workspace`, and speaks MCP
+over stdio. The scan **writes** the databases; the MCP server **reads** them. One repo on disk is the
+single source of truth.
+
+```mermaid
+flowchart LR
+ app["Consuming app
+
+- :material-download:{ .lg .middle } __Installation__
+
+ ---
+
+ Docker, PyPI, GitHub, or a local checkout - pick the path that fits.
+
+ [:octicons-arrow-right-24: Install WhyGraph](installation.md)
+
+- :material-rocket-launch:{ .lg .middle } __Quickstart__
+
+ ---
+
+ Init, scan, wire an editor - the happy path in four commands.
+
+ [:octicons-arrow-right-24: Quickstart](quickstart.md)
+
+
diff --git a/docs/getting-started/installation.md b/docs/getting-started/installation.md
new file mode 100644
index 0000000..47e9741
--- /dev/null
+++ b/docs/getting-started/installation.md
@@ -0,0 +1,69 @@
+# Installation
+
+WhyGraph follows a one-global-install, use-anywhere model - like `npx`, but for Python. You install
+the package once; that puts `whygraph` and `whygraph-mcp` on your `PATH`. Then
+`whygraph init --agent ` wires each project so its editor can launch the MCP server.
+
+Pick the path that fits where you are.
+
+=== "Docker (recommended)"
+
+ The host needs **only Docker** - no Python, Node, `gh`, or CodeGraph. A tiny shim runs everything
+ inside one published image.
+
+ ```bash
+ curl -fsSL https://raw.githubusercontent.com/mtrdesign/whygraph/main/scripts/install.sh | sh
+ ```
+
+ This drops `whygraph` and `whygraph-mcp` shims on your `PATH`. Each wraps a
+ `docker run --rm -v "$PWD:/workspace" … ghcr.io/mtrdesign/whygraph` against the current repo. The
+ container is ephemeral per command. See [Run with Docker](../deploy/docker.md) for the full story.
+
+=== "PyPI"
+
+ ```bash
+ uv tool install whygraph # or: pipx install whygraph
+ ```
+
+ !!! warning "Not yet published"
+ WhyGraph isn't on PyPI yet. Use the GitHub or local-checkout paths until v1 ships.
+
+=== "GitHub"
+
+ Install straight from the repo - latest `main`, a feature branch, or a tag:
+
+ ```bash
+ # Latest from main:
+ uv tool install "git+https://github.com/mtrdesign/whygraph.git"
+
+ # A specific branch:
+ uv tool install "git+https://github.com/mtrdesign/whygraph.git@feature/some-branch"
+
+ # A specific tag (once tagged):
+ uv tool install "git+https://github.com/mtrdesign/whygraph.git@v1.0.0"
+ ```
+
+ Re-running upgrades in place. To switch refs, add `--force`. `pipx` accepts the same URLs.
+
+=== "Local checkout"
+
+ For contributors who want their edits to show up immediately:
+
+ ```bash
+ git clone https://github.com/mtrdesign/whygraph.git
+ uv tool install --editable ./whygraph
+ ```
+
+ `--editable` skips the reinstall on every change.
+
+## Verify
+
+```bash
+whygraph version
+which whygraph-mcp
+```
+
+Both should resolve to your global tool install. With the Docker shim, `which whygraph-mcp` points at
+the shim script on your `PATH`.
+
+Next: [scan a repo and wire your editor.](quickstart.md)
diff --git a/docs/getting-started/quickstart.md b/docs/getting-started/quickstart.md
new file mode 100644
index 0000000..0b2257c
--- /dev/null
+++ b/docs/getting-started/quickstart.md
@@ -0,0 +1,82 @@
+# Quickstart
+
+You've [installed WhyGraph](installation.md). Now point it at a repo. This is the happy path: init,
+scan, wire an editor, sanity-check.
+
+## 1. Initialize
+
+From the repo you want to analyze:
+
+```bash
+whygraph init
+```
+
+This creates `.whygraph/whygraph.db`, writes a commented `whygraph.example.toml`, and adds the right
+`.gitignore` entries. It's idempotent - run it again any time. It does *not* index CodeGraph yet;
+that's the next step.
+
+## 2. Scan
+
+```bash
+whygraph scan
+```
+
+`scan` walks your git history, optionally crawls the remote for PRs and issues, refreshes the
+CodeGraph index, and writes a per-commit LLM description. That fills `.whygraph/whygraph.db` with the
+evidence WhyGraph serves.
+
+!!! note "The remote crawl is off by default"
+ A fresh scan stays git-only and needs no token, because `[scan].provider` defaults to `"off"`. To
+ pull PRs and issues, set `provider = "github"` (or `"auto"`) in `whygraph.toml`.
+
+For a fast, offline pass - no remote calls, no LLM - skip both phases:
+
+```bash
+whygraph scan --no-remote --no-llm-descriptions
+```
+
+Descriptions backfill lazily later, so this is a fine way to get started quickly. See
+[Scanning your repo](../guide/scanning.md) for what each phase does.
+
+## 3. Wire your editor
+
+Register the MCP server with your agent. For Claude Code:
+
+```bash
+whygraph init --agent claude
+```
+
+That writes `.mcp.json` at the repo root and copies the bundled assets into `.claude/`. Other agents
+work the same way - `--agent cursor`, `--agent vscode`, `--agent codex`. See
+[Wiring your editor](../guide/editors.md) for each one's config path.
+
+## 4. Sanity-check the server
+
+```bash
+whygraph-mcp # Ctrl-C to exit
+```
+
+If it launches without error, your editor can launch it too. That's it - ask your assistant why a
+function exists, and WhyGraph answers from history.
+
+## Where to next
+
+
+
+- :material-lightbulb-on:{ .lg .middle } __Concepts__
+
+ ---
+
+ Evidence, rationale cards, and the CodeGraph split.
+
+ [:octicons-arrow-right-24: Concepts](../guide/concepts.md)
+
+- :material-connection:{ .lg .middle } __Using WhyGraph__
+
+ ---
+
+ How an agent calls the tools mid-task.
+
+ [:octicons-arrow-right-24: MCP usage](../guide/mcp-usage.md)
+
+
diff --git a/docs/guide/concepts.md b/docs/guide/concepts.md
new file mode 100644
index 0000000..288b253
--- /dev/null
+++ b/docs/guide/concepts.md
@@ -0,0 +1,59 @@
+# Concepts
+
+WhyGraph has two core ideas: **evidence** (the raw history behind code) and **rationale** (an
+LLM-synthesized explanation built from that evidence). Understand these two, and the rest of the tool
+follows.
+
+## Evidence
+
+Evidence is the factual record: the commits that touched a chunk of code, the blame behind each line,
+the pull requests that merged it, and the issues those PRs closed. WhyGraph collects it during
+[`scan`](scanning.md) and links it together, so one lookup returns the whole chain.
+
+You reach evidence two ways, because there are two questions to ask:
+
+- **`whygraph_evidence_for`** - "which commits authored *these specific lines*?" Line-blame-driven and
+ anchored to HEAD. Best when you have a precise range or a symbol.
+- **`whygraph_area_history`** - "which commits ever touched *this file*, or anything that became this
+ file?" It walks the rename chain, so it reaches code that's since been deleted, moved, or fully
+ rewritten - commits that blame physically can't surface.
+
+The two reinforce each other. Evidence keeps line-level precision; area history reaches further back.
+
+## Rationale cards
+
+A rationale card is WhyGraph's answer to "why does this exist?" It takes the evidence bundle, hands it
+to the configured LLM, and gets back a structured card with exactly five fields:
+
+- **purpose** - what this code is for.
+- **why** - why it was written this way.
+- **constraints** - what it must preserve.
+- **tradeoffs** - what was given up, and for what.
+- **risks** - what could break if you change it.
+
+The card comes back with provenance too - `model`, `provider`, `cached_at` - and an `evidence_count`
+summarizing how many commits, PRs, and issues fed it.
+
+!!! note "Five fields, nothing more"
+ A card carries those five narrative fields and nothing else - no extra score or rating. The
+ rationale is the evidence-grounded explanation, full stop.
+
+### Caching
+
+Cards are **persistently cached**, keyed by content - the target, the evidence bundle, the provider,
+and the model. Generate a card once and the next identical lookup is a sub-second database read. Change
+the underlying code (so the evidence shifts) and the next call regenerates. You pay the LLM cost only
+when something actually changed.
+
+## The CodeGraph split
+
+WhyGraph sits on top of CodeGraph and stays out of its lane:
+
+| Layer | Owns |
+|---|---|
+| **CodeGraph** | "what's connected to what" - callers, callees, `find_symbols`, type hierarchy |
+| **WhyGraph** | "why it exists and when it changed" - evidence, rationale, area history |
+
+When you target a symbol by `qualified_name`, WhyGraph asks CodeGraph to resolve it to a file and line
+range, then layers its own history on top. It exposes no graph-traversal tools of its own - for that,
+call CodeGraph directly.
diff --git a/docs/guide/editors.md b/docs/guide/editors.md
new file mode 100644
index 0000000..abdb728
--- /dev/null
+++ b/docs/guide/editors.md
@@ -0,0 +1,58 @@
+# Wiring your editor
+
+`whygraph-mcp` is a standalone MCP server, so any agent that speaks MCP can use it.
+`whygraph init --agent X` writes the right config to the right place for each one.
+
+Run it from the repo you want WhyGraph to analyze:
+
+```bash
+whygraph init --agent claude
+```
+
+## Supported agents
+
+Four agents are supported. **All of them are project-scoped** - the config file is written or merged
+inside the repo, so you can commit it and every teammate's editor picks it up.
+
+| `--agent` | Editor | Config file |
+|---|---|---|
+| `claude` | Claude Code | `.mcp.json` (repo root) |
+| `cursor` | Cursor | `.cursor/mcp.json` |
+| `vscode` (alias `copilot`) | VS Code / GitHub Copilot | `.vscode/mcp.json` |
+| `codex` | OpenAI Codex | `.codex/config.toml` |
+
+Run `whygraph init --list-agents` to print these paths for your own checkout.
+
+The generated config launches `whygraph-mcp` by bare command name, so the same checked-in file works
+for everyone who has WhyGraph installed - no absolute paths to scrub.
+
+## Claude Code assets
+
+`--agent claude` does one extra thing: it copies a bundled asset tree into `.claude/`. Re-running
+leaves your existing files alone; pass `--force` to overwrite them.
+
+```bash
+whygraph init --agent claude --no-install-assets # MCP wiring only, skip the .claude/ copy
+whygraph init --agent claude --force # overwrite existing .claude/ files
+```
+
+## Useful flags
+
+| Flag | What it does |
+|---|---|
+| `--print` | Print the MCP snippet to stdout instead of writing any file. Good for pasting by hand. |
+| `--list-agents` | List supported agents and their config paths, then exit. |
+| `--install-assets / --no-install-assets` | Copy (or skip) the agent's bundled assets. Default: copy. No-op for agents with no asset tree. |
+| `--skip-preflight` | Skip the host-tool diagnostics. For known-good scripted environments. |
+| `--force` | Overwrite existing asset files in the destination directory. |
+
+## Verify
+
+After wiring, confirm the server launches:
+
+```bash
+whygraph-mcp # Ctrl-C to exit
+```
+
+If it starts cleanly, your editor can start it too. Next, see how an agent
+[actually calls the tools](mcp-usage.md).
diff --git a/docs/guide/index.md b/docs/guide/index.md
new file mode 100644
index 0000000..8a1ee6b
--- /dev/null
+++ b/docs/guide/index.md
@@ -0,0 +1,46 @@
+# User Guide
+
+You've scanned a repo and wired an editor. This guide explains how the pieces fit together - and how
+to get the most out of each.
+
+The flow is simple. You **scan** a repo to build the evidence database and refresh the CodeGraph
+index. Your editor launches the **MCP server**, which reads that database. As you work, the server's
+**tools, resources, and prompts** answer "why does this code exist?" from history.
+
+Start with the concepts, then dig into whichever piece you need.
+
+
+
+- :material-lightbulb-on:{ .lg .middle } __Concepts__
+
+ ---
+
+ Evidence vs rationale, and how WhyGraph splits work with CodeGraph.
+
+ [:octicons-arrow-right-24: Concepts](concepts.md)
+
+- :material-radar:{ .lg .middle } __Scanning your repo__
+
+ ---
+
+ The scan phases, every flag, and the keep-fresh git hooks.
+
+ [:octicons-arrow-right-24: Scanning](scanning.md)
+
+- :material-application-edit:{ .lg .middle } __Wiring your editor__
+
+ ---
+
+ Per-agent setup for Claude Code, Cursor, VS Code, and Codex.
+
+ [:octicons-arrow-right-24: Editors](editors.md)
+
+- :material-connection:{ .lg .middle } __Using WhyGraph (MCP)__
+
+ ---
+
+ How an agent calls the tools, resources, and prompts mid-task.
+
+ [:octicons-arrow-right-24: MCP usage](mcp-usage.md)
+
+
diff --git a/docs/guide/mcp-usage.md b/docs/guide/mcp-usage.md
new file mode 100644
index 0000000..c05692a
--- /dev/null
+++ b/docs/guide/mcp-usage.md
@@ -0,0 +1,50 @@
+# Using WhyGraph (MCP)
+
+Once your editor is wired, WhyGraph works through MCP - your assistant calls its tools mid-task, the
+way it would any other tool. This page shows what's available and when to reach for each. For exact
+signatures, see the [MCP reference](../reference/mcp.md).
+
+## The tools
+
+Three tools cover the two questions - evidence and rationale.
+
+**Reaching for history?** Use the evidence tools:
+
+- `whygraph_evidence_for(path, line_start, line_end | qualified_name, limit=20)` - the commits, PRs,
+ and issues behind a specific range or symbol. Line-blame-driven, anchored to HEAD.
+- `whygraph_area_history(path, limit=20, include_renames=True)` - every commit that touched a file or
+ its rename predecessors. Use it when the code moved, got deleted, or was rewritten and blame comes
+ up short.
+
+**Reaching for the *why*?** Use the rationale tool:
+
+- `whygraph_rationale_brief(path, line_start, line_end | qualified_name)` - a structured card:
+ purpose, why, constraints, tradeoffs, risks. Cached, so a repeat call is instant.
+
+A typical flow: before editing a function, your assistant calls `whygraph_rationale_brief` to ground
+itself in intent. If the card comes back thin, it falls back to `whygraph_evidence_for` for the raw
+history.
+
+## The resources
+
+Read-only JSON, addressed by URI - handy when you already know the commit, PR, or issue:
+
+- `whygraph://commit/{sha}` - a commit and the PRs that contain it.
+- `whygraph://pr/{number}` - a PR and the issues it closes.
+- `whygraph://issue/{number}` - an issue and the PRs that close it.
+- `whygraph://repo/overview` - repo-level summary: counts, scan freshness, coverage, top contributors.
+
+## The prompts
+
+Prompts are ready-made recipes that wire the tools into a workflow:
+
+- `whygraph_pre_edit_brief` - gather rationale and history before you edit, so the change respects
+ constraints and avoids known risks.
+- `whygraph_why_was_this_written` - recover the original intent behind a chunk of code.
+- `whygraph_triage_commit` - summarize what one commit did and why, from its PR and closing issues.
+
+## What WhyGraph won't do
+
+WhyGraph has **no graph-traversal tools** - no callers, no callees, no symbol search. That's
+CodeGraph's job, on purpose. When your assistant needs "who calls this?", it asks CodeGraph directly.
+WhyGraph stays focused on why the code exists and how it got here.
diff --git a/docs/guide/scanning.md b/docs/guide/scanning.md
new file mode 100644
index 0000000..962ad3e
--- /dev/null
+++ b/docs/guide/scanning.md
@@ -0,0 +1,75 @@
+# Scanning your repo
+
+`whygraph scan` builds the evidence database. It's the command you run after `init`, and again
+whenever you want WhyGraph current. It's idempotent - each run picks up new commits and backfills
+what's missing.
+
+```bash
+whygraph scan
+```
+
+## What a scan does
+
+A scan runs several phases:
+
+1. **Git crawl** - walks first-parent history and records commits, authors, and blame.
+2. **Remote crawl** *(optional)* - pulls PRs and issues per `[scan].provider`, and links them to
+ commits. Off unless you enable a provider.
+3. **CodeGraph index refresh** - `codegraph init -i` on the first run, `codegraph sync` after. Runs
+ concurrently with the crawl. A failure here warns rather than aborting, since only the rationale
+ and evidence *tools* need CodeGraph.
+4. **LLM descriptions** - writes a short description of each commit's diff with the configured
+ provider.
+
+It also handles **squash-merge recovery**: when a PR was squash-merged, `--pr-origins` does one
+targeted `git fetch` of the PR's original head, so its feature-branch commits enrich the evidence
+without polluting area history.
+
+## Flags
+
+| Flag | Default | What it does |
+|---|---|---|
+| `--no-llm-descriptions` | off | Skip the per-commit LLM phase. Git and GitHub crawlers still run; descriptions backfill lazily and on a later full scan. |
+| `--codegraph / --no-codegraph` | on | Refresh the CodeGraph index concurrently with the crawl. |
+| `--codegraph-image TEXT` | pinned tag | Override the Docker image for the CodeGraph fallback. Ignored when a local `codegraph` binary is found. |
+| `--remote / --no-remote` | on | Crawl the remote for PRs and issues per `[scan].provider`. `--no-remote` is a fast, offline, token-free scan. |
+| `--pr-origins / --no-pr-origins` | on | Recover a squash-merged PR's original commits. Needs the network, so it's skipped under `--no-remote`. |
+
+A common fast pass while iterating:
+
+```bash
+whygraph scan --no-remote --no-llm-descriptions
+```
+
+!!! tip "Lazy backfill"
+ Skipping descriptions doesn't lose them. The MCP tools backfill a commit's description on demand
+ when they need it, and a later full `whygraph scan` fills in the rest. Start fast, enrich later.
+
+## Keep it fresh
+
+Don't want to re-scan by hand? Install git hooks once, and new commits refresh WhyGraph and CodeGraph
+on the fly:
+
+```bash
+whygraph hooks install
+```
+
+This wires `post-commit`, `post-merge`, and `post-rewrite` to run
+`whygraph scan --no-remote --no-llm-descriptions` **in the background**. Git history and a CodeGraph
+`sync` only - no LLM, no remote calls - so commits stay instant and the scan is offline and
+token-free.
+
+The hooks are detached and single-flight: rapid commits coalesce instead of stacking, and the latest
+`HEAD` always wins. An existing hook of your own is appended to behind a sentinel guard, never
+overwritten.
+
+Check or remove them any time:
+
+```bash
+whygraph hooks status
+whygraph hooks uninstall
+```
+
+!!! note "Hooks stay fast on purpose"
+ The hooks deliberately skip the remote and LLM phases so they never slow a commit. For PRs,
+ issues, and fresh descriptions, run a full `whygraph scan` now and then.
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 0000000..0607132
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,87 @@
+---
+hide:
+ - navigation
+ - toc
+---
+
+# WhyGraph
+
+
+Explains why code exists, not just what it does.
+
+
+A rationale layer over [CodeGraph](https://github.com/colbymchenry/codegraph). It mines your git
+history and GitHub for the story behind each line - the commits, pull requests, and issues that put
+it there - and serves that story to any AI editor over MCP.
+
+[Get started](getting-started/quickstart.md){ .md-button .md-button--primary }
+[View on GitHub](https://github.com/mtrdesign/whygraph){ .md-button }
+
+---
+
+
+
+- :material-history:{ .lg .middle } __Evidence from your history__
+
+ ---
+
+ For any chunk of code, WhyGraph pulls the commits that touched it, the blame behind each line,
+ the PRs that merged it, and the issues those PRs closed - already linked together.
+
+ [:octicons-arrow-right-24: Concepts](guide/concepts.md)
+
+- :material-card-text-outline:{ .lg .middle } __Rationale cards__
+
+ ---
+
+ Ask why a symbol exists and get a structured card: purpose, why, constraints, tradeoffs, and
+ risks. Each card is cached, so the second lookup is instant.
+
+ [:octicons-arrow-right-24: Using WhyGraph](guide/mcp-usage.md)
+
+- :material-connection:{ .lg .middle } __MCP-native__
+
+ ---
+
+ `whygraph-mcp` is a standard MCP server over stdio. Claude Code, Cursor, VS Code, Codex - any
+ editor that speaks MCP can call it. One command wires each project.
+
+ [:octicons-arrow-right-24: Wire your editor](guide/editors.md)
+
+- :material-docker:{ .lg .middle } __Only Docker required__
+
+ ---
+
+ No Python, Node, `gh`, or CodeGraph on your host. A tiny shim runs everything inside one image,
+ ephemeral per command. Install, init, scan - done.
+
+ [:octicons-arrow-right-24: Run with Docker](deploy/docker.md)
+
+- :material-graph-outline:{ .lg .middle } __Composes with CodeGraph__
+
+ ---
+
+ CodeGraph answers "what's connected to what". WhyGraph answers "why it exists and when it
+ changed". Run both; each stays focused on its own job.
+
+ [:octicons-arrow-right-24: Getting started](getting-started/index.md)
+
+- :material-server-network:{ .lg .middle } __Git analysis as a service__
+
+ ---
+
+ The MCP server isn't just for editors. Real applications can connect to it for git-based
+ analysis of a target repo, reading the same cached data your scan writes.
+
+ [:octicons-arrow-right-24: WhyGraph as a service](deploy/service.md)
+
+
+
+## Who it's for
+
+You're dropping into an unfamiliar codebase, or editing code you wrote months ago and no longer
+remember. The *what* is in front of you; the *why* is buried in history. WhyGraph surfaces that why
+right where your AI assistant works, so an edit respects the original intent instead of rediscovering
+it the hard way.
+
+Ready? [Start with the Quickstart.](getting-started/quickstart.md)
diff --git a/docs/reference/cli.md b/docs/reference/cli.md
new file mode 100644
index 0000000..add9123
--- /dev/null
+++ b/docs/reference/cli.md
@@ -0,0 +1,95 @@
+# CLI reference
+
+Every WhyGraph command and its flags. Run `whygraph --help` to see the same text from your
+own install. There are five commands.
+
+```console
+$ whygraph --help
+Commands:
+ analyze Describe a commit's diff with the configured LLM.
+ hooks Manage opt-in git hooks that auto-rescan on new commits.
+ init Initialize the WhyGraph database under .whygraph/whygraph.db.
+ scan Run the source crawlers, then describe each commit with the LLM.
+ version Print installed whygraph version.
+```
+
+## `whygraph version`
+
+Print the installed package version. No options.
+
+```bash
+whygraph version
+```
+
+## `whygraph init`
+
+Bootstrap the WhyGraph database under `.whygraph/whygraph.db`, write a committable
+`whygraph.example.toml` documenting every tunable, and add the right `.gitignore` entries. It's
+idempotent - re-running on an initialized project just confirms both databases are present.
+
+`init` does **not** index CodeGraph. That happens on [`scan`](#whygraph-scan).
+
+With `--agent X`, it also wires the WhyGraph MCP server into that agent's config. All supported
+agents are project-scoped, so the config file is written inside the repo.
+
+| Option | Description |
+|---|---|
+| `--agent [claude\|codex\|copilot\|cursor\|vscode]` | Wire the MCP server into the named agent's config. |
+| `--print` | Print the MCP snippet to stdout instead of writing any config file. |
+| `--list-agents` | List supported agents (with config-file paths) and exit. |
+| `--install-assets / --no-install-assets` | Copy the chosen agent's bundled assets into the project. Default: enabled. No-op for agents that ship no asset tree. |
+| `--skip-preflight` | Skip the host-tool diagnostics that normally run first. For known-good scripted environments. |
+| `--force` | When installing assets, overwrite existing files in the agent's destination directory. |
+
+See [Wiring your editor](../guide/editors.md) for the per-agent paths.
+
+## `whygraph scan`
+
+Run the source crawlers, then describe each commit with the configured LLM. This is the command that
+populates `.whygraph/whygraph.db` and refreshes the CodeGraph index. It's idempotent - re-running
+picks up new commits and backfills what's missing.
+
+| Option | Default | Description |
+|---|---|---|
+| `--no-llm-descriptions` | off | Skip the per-commit LLM description phase. The git and GitHub crawlers still run; descriptions backfill lazily on demand and on a later full scan. |
+| `--codegraph / --no-codegraph` | on | Refresh the CodeGraph index concurrently with the crawl - `codegraph sync` when an index exists, `codegraph init -i` on first run. A failure here warns rather than aborting. |
+| `--codegraph-image TEXT` | pinned tag | Override the Docker image used for the CodeGraph refresh fallback. Ignored when a local `codegraph` binary is found. |
+| `--remote / --no-remote` | on | Crawl the source-control remote (GitHub PRs / issues) per `[scan].provider`. `--no-remote` skips it for a fast, offline, token-free scan. |
+| `--pr-origins / --no-pr-origins` | on | Recover a squash-merged PR's original feature-branch commits via one targeted `git fetch`. Needs the network, so it's skipped under `--no-remote`. |
+
+See [Scanning your repo](../guide/scanning.md) for what each phase does.
+
+## `whygraph analyze`
+
+Describe a single commit's diff with the configured LLM and **print** the result. Unlike `scan`, it
+doesn't persist anything.
+
+```bash
+whygraph analyze [BASELINE]
+```
+
+`TARGET` is the commit being analyzed. With no `BASELINE`, it's compared to its parent; with a
+`BASELINE`, the diff analyzed is `git diff BASELINE..TARGET`.
+
+!!! note "Scan first"
+ Every commit named on the command line must already exist in the WhyGraph database. Run
+ `whygraph scan` before `whygraph analyze`.
+
+## `whygraph hooks`
+
+Manage opt-in git hooks that auto-rescan on new commits. There's no daemon - the hooks run a fast,
+background, offline scan as you commit.
+
+| Subcommand | Description |
+|---|---|
+| `install` | Install the auto-rescan hooks into the current repository. Idempotent and non-clobbering - it appends to a foreign hook behind a sentinel guard. |
+| `status` | Report whether the auto-rescan hooks are installed. |
+| `uninstall` | Remove the auto-rescan hooks, leaving any foreign hook content intact. |
+
+```bash
+whygraph hooks install
+```
+
+The hooks wire `post-commit`, `post-merge`, and `post-rewrite` to run
+`whygraph scan --no-remote --no-llm-descriptions` in the background. See
+[Keep it fresh](../guide/scanning.md#keep-it-fresh) for the details.
diff --git a/docs/reference/configuration.md b/docs/reference/configuration.md
new file mode 100644
index 0000000..51abbc7
--- /dev/null
+++ b/docs/reference/configuration.md
@@ -0,0 +1,110 @@
+# Configuration
+
+WhyGraph reads an optional `whygraph.toml` at your repo root. Every field has a built-in default, so
+an unedited file behaves exactly as if none were present. `whygraph init` scaffolds a fully-commented
+`whygraph.example.toml` for you - copy it to `whygraph.toml` and edit what you need.
+
+!!! warning "`whygraph.toml` is gitignored - never commit a token"
+ `init` adds `whygraph.toml` to `.gitignore` precisely because it can hold API keys. Keep it that
+ way. Use `whygraph.example.toml` (committed) for documentation, `whygraph.toml` (ignored) for
+ secrets.
+
+## The full tree
+
+The values shown are the defaults.
+
+```toml
+log_level = "INFO" # DEBUG | INFO | WARN | ERROR | CRITICAL
+
+[scan]
+max_workers = 2 # parallel LLM calls in the diff-analyzer crawler
+provider = "off" # source-control backend for the PR/issue crawl:
+ # "off" - skip the remote crawl (default)
+ # "github" - pull PRs/issues from the GitHub remote
+ # "auto" - detect from the remote URL (github only, for now)
+remote = "origin" # git remote whose URL is inspected for provider="auto"
+# token = "ghp_..." # GitHub token for the gh CLI. Default: read GH_TOKEN /
+ # GITHUB_TOKEN from env (or an existing `gh auth login`).
+
+[analyze]
+provider = "anthropic" # which [llm.*] adapter writes per-commit descriptions
+# model = "claude-haiku-4-5" # override the provider's model for analysis only
+# max_diff_chars = 50000 # diff truncated past this length before prompting
+# large_commit_file_count = 30 # commits touching more files are described per-file on demand
+# pr_origin_min_commits = 5 # recover a squash-merged PR's original commits past this size
+# timeout_sec = 60 # per-call timeout; default: the adapter's own
+
+[rationale]
+provider = "anthropic" # which [llm.*] adapter writes the rationale card
+# model = "claude-haiku-4-5" # override the provider's model for rationale only
+# timeout_sec = 60 # per-call timeout; default: the adapter's own
+# pr_roster_max_commits = 30 # squashed-commit headlines shown per PR in the prompt
+# pr_discussion_max_comments = 20 # PR comments shown per PR in the prompt
+# pr_comment_max_chars = 500 # each PR comment clipped to this length
+
+# Override default DB locations (resolved relative to this file):
+# whygraph_db = ".whygraph/whygraph.db"
+# codegraph_db = ".codegraph/codegraph.db"
+
+# Optional rotating file log. Console (stderr) logging is always on.
+# [logging]
+# file = ".whygraph/logs/whygraph.log"
+# level = "DEBUG" # default: inherit top-level log_level
+# max_bytes = 5_000_000
+# backup_count = 3
+
+[llm.anthropic]
+model = "claude-opus-4-7"
+# api_key = "sk-ant-..." # default: read ANTHROPIC_API_KEY from env
+timeout_sec = 60
+
+[llm.openai]
+model = "gpt-4o"
+# api_key = "sk-..." # default: read OPENAI_API_KEY from env
+# base_url = "..." # default: https://api.openai.com/v1
+timeout_sec = 60
+
+[llm.deepseek]
+model = "deepseek-chat"
+# api_key = "sk-..." # default: read DEEPSEEK_API_KEY from env
+timeout_sec = 60
+
+[llm.ollama]
+model = "llama3"
+# host = "http://localhost:11434"
+timeout_sec = 120
+
+# `claude_cli` (Python attribute) and `claude-cli` (TOML idiom) both parse.
+[llm.claude_cli]
+model = "claude-opus-4-7"
+# api_key = "sk-ant-..." # default: subscription billing (strips the env var)
+timeout_sec = 120
+```
+
+## Section by section
+
+| Section | What it controls |
+|---|---|
+| top-level `log_level` | Console log verbosity. |
+| `[scan]` | The crawl: parallelism, which remote provider to use, the git remote name, and an optional pinned GitHub token. |
+| `[analyze]` | The per-commit LLM diff descriptions written during `scan` - provider, model, and the truncation / per-file thresholds. |
+| `[rationale]` | The `whygraph_rationale_brief` card - provider, model, and how much of a squash-merged PR is rendered into the prompt. |
+| `whygraph_db` / `codegraph_db` | Override either database path. |
+| `[logging]` | An optional rotating file log, in addition to the always-on stderr log. |
+| `[llm.*]` | Per-provider client settings - model, key, timeout, and `base_url` / `host` where relevant. |
+
+## Environment variables
+
+Omit an `api_key` from an `[llm.*]` table and WhyGraph reads the standard environment variable
+instead.
+
+| Variable | Used for |
+|---|---|
+| `ANTHROPIC_API_KEY` | The `anthropic` LLM adapter. |
+| `OPENAI_API_KEY` | The `openai` LLM adapter. |
+| `DEEPSEEK_API_KEY` | The `deepseek` LLM adapter. |
+| `GH_TOKEN` / `GITHUB_TOKEN` | The `gh` CLI during the remote crawl, when `[scan].token` is unset. |
+
+!!! tip "Provider keys degrade gracefully"
+ Missing a key for the analysis or rationale phase isn't fatal - that phase skips, and the rest of
+ the scan still runs. Descriptions and cards backfill once a credential is available.
diff --git a/docs/reference/index.md b/docs/reference/index.md
new file mode 100644
index 0000000..c47ccae
--- /dev/null
+++ b/docs/reference/index.md
@@ -0,0 +1,40 @@
+# Reference
+
+The exact surface - every command, tool, resource, and config key. This section is hand-written
+against the running code, so it stays in step with what `whygraph` actually does. Pick a page:
+
+
+
+- :material-console:{ .lg .middle } __CLI__
+
+ ---
+
+ Every command and flag, straight from `--help`: `init`, `scan`, `analyze`, `hooks`, `version`.
+
+ [:octicons-arrow-right-24: CLI reference](cli.md)
+
+- :material-connection:{ .lg .middle } __MCP surface__
+
+ ---
+
+ The three tools, four resources, and three prompts that `whygraph-mcp` registers.
+
+ [:octicons-arrow-right-24: MCP reference](mcp.md)
+
+- :material-cog:{ .lg .middle } __Configuration__
+
+ ---
+
+ The full `whygraph.toml` tree and the environment variables WhyGraph reads.
+
+ [:octicons-arrow-right-24: Configuration](configuration.md)
+
+- :material-source-branch:{ .lg .middle } __Providers__
+
+ ---
+
+ Which source-control hosts the remote crawl supports today, and what's coming.
+
+ [:octicons-arrow-right-24: Providers](providers.md)
+
+
diff --git a/docs/reference/mcp.md b/docs/reference/mcp.md
new file mode 100644
index 0000000..27815eb
--- /dev/null
+++ b/docs/reference/mcp.md
@@ -0,0 +1,109 @@
+# MCP surface
+
+`whygraph-mcp` registers three tools, four resources, and three prompts. That's the whole surface -
+deliberately narrow. WhyGraph owns "why this exists and when it changed"; graph traversal
+("what's connected to what") stays with CodeGraph.
+
+For a usage-first walkthrough of how an agent calls these mid-task, see
+[Using WhyGraph](../guide/mcp-usage.md).
+
+## Tools
+
+### `whygraph_evidence_for`
+
+Historical evidence - commits, PRs, and closing issues - for a chunk of code. Line-blame-driven and
+anchored to HEAD.
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `path` | str | - | Source file path, relative to the repo root. |
+| `line_start` | int | - | First line of the chunk (1-indexed, inclusive). |
+| `line_end` | int | - | Last line of the chunk (1-indexed, inclusive). |
+| `qualified_name` | str | - | Fully-qualified symbol name. Use instead of `path`/lines when you know the symbol. CodeGraph resolves it to a file/line range. |
+| `limit` | int | `20` | Cap on the number of commits returned. |
+
+Returns `{ "target": {...}, "evidence": [ { "commit", "pull_requests", "issues", "source" }, ... ] }`.
+
+### `whygraph_area_history`
+
+Every commit that touched a file path - or any path it was renamed from. Where `evidence_for` is
+line-blame-driven, `area_history` reaches commits for code that's since been deleted, moved, or
+fully rewritten.
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `path` | str | *required* | The file path, as it appears at HEAD (or any commit - the rename chain is bidirectional). |
+| `limit` | int | `20` | Cap on commits returned, newest first. |
+| `include_renames` | bool | `true` | Walk the `renamed_from` chain to include commits that touched historical names. |
+
+Returns `{ "path", "include_renames", "evidence": [...] }`, using the same evidence shape as
+`whygraph_evidence_for`.
+
+### `whygraph_rationale_brief`
+
+Generate a structured rationale card explaining why a chunk of code exists. It gathers the evidence,
+optionally enriches it with CodeGraph symbol context, and asks the configured LLM to synthesize the
+card. Cards are cached, so a repeat call on unchanged code is a fast database read.
+
+| Parameter | Type | Description |
+|---|---|---|
+| `path` | str | Source file path, relative to the repo root. |
+| `line_start` | int | First line of the chunk. |
+| `line_end` | int | Last line of the chunk. |
+| `qualified_name` | str | Fully-qualified symbol name, instead of `path`/lines. |
+
+Returns the card:
+
+```json
+{
+ "target": { "...": "..." },
+ "purpose": "...",
+ "why": "...",
+ "constraints": ["..."],
+ "tradeoffs": ["..."],
+ "risks": ["..."],
+ "model": "claude-opus-4-7",
+ "provider": "anthropic",
+ "cached_at": "2026-06-11T12:00:00Z",
+ "evidence_count": { "commits": 8, "prs": 3, "issues": 2 }
+}
+```
+
+The card carries exactly five narrative fields - **purpose, why, constraints, tradeoffs, risks** -
+plus provenance (`model`, `provider`, `cached_at`) and an `evidence_count` summary.
+
+!!! note "Calls the LLM on a cache miss"
+ On a miss, this hits the configured provider and may take several seconds. A hit is sub-second.
+ Generation needs a credential - see [Configuration](configuration.md).
+
+## Resources
+
+Read-only, JSON, addressed by URI.
+
+| URI | Name | Description |
+|---|---|---|
+| `whygraph://commit/{sha}` | `whygraph_commit` | A scanned commit and the pull requests that contain it (closing issues not inlined). |
+| `whygraph://pr/{number}` | `whygraph_pull_request` | A pull request and the issues it closes. Includes full `commit_titles` and `comments`. |
+| `whygraph://issue/{number}` | `whygraph_issue` | An issue and the pull requests that close it. |
+| `whygraph://repo/overview` | `whygraph_repo_overview` | Repo-level summary: row counts, commit date range, scan freshness, LLM-description coverage, top contributors. |
+
+## Prompts
+
+Orchestration recipes that wire the tools into a workflow.
+
+| Name | Title | Arguments | What it does |
+|---|---|---|---|
+| `whygraph_pre_edit_brief` | Pre-edit brief | `path` / `line_start` / `line_end` / `qualified_name` | Before you edit, gather rationale and history so the edit respects constraints and avoids known risks. |
+| `whygraph_why_was_this_written` | Why was this written? | `path` / `line_start` / `line_end` / `qualified_name` | Recover the original intent behind a chunk of code from its commits, PRs, and closing issues. |
+| `whygraph_triage_commit` | Triage a commit | `sha` | Summarize what one commit did and why, using its linked PR and closing issues. |
+
+## Composition with CodeGraph
+
+WhyGraph exposes no graph-traversal tools on purpose. The split:
+
+| Layer | Owns |
+|---|---|
+| **CodeGraph** | "what is connected to what" - callers, callees, symbol resolution, type hierarchy. |
+| **WhyGraph** | "why does this exist and when did it change" - evidence, rationale, history. |
+
+For traversal mid-conversation, call CodeGraph's own tools directly.
diff --git a/docs/reference/providers.md b/docs/reference/providers.md
new file mode 100644
index 0000000..1f9dd81
--- /dev/null
+++ b/docs/reference/providers.md
@@ -0,0 +1,48 @@
+# Source control providers
+
+WhyGraph's remote crawl enriches your scan with pull requests and issues. You choose the backend with
+`[scan].provider` in `whygraph.toml`. Today there's one supported provider - GitHub - with others on
+the way.
+
+## GitHub - supported
+
+Set the provider to `github` to pull PRs and issues from the GitHub remote:
+
+```toml
+[scan]
+provider = "github"
+```
+
+Or let WhyGraph detect it from your remote URL:
+
+```toml
+[scan]
+provider = "auto" # detect from the remote (github only, for now)
+remote = "origin" # the git remote whose URL is inspected
+```
+
+The crawl uses the `gh` CLI, so you need it authenticated. Provide a token one of three ways:
+
+- An existing `gh auth login`.
+- `GH_TOKEN` or `GITHUB_TOKEN` in your environment.
+- `[scan].token` in `whygraph.toml` - handy when one container scans repos across different orgs.
+
+!!! note "Off by default"
+ `provider` defaults to `"off"`, so a fresh scan stays git-only and needs no token. Opt into the
+ remote crawl by setting `github` or `auto`. You can also skip it per-run with
+ `whygraph scan --no-remote`.
+
+## Upcoming
+
+Other hosts are planned, not yet built. Until they land, point WhyGraph at a GitHub remote or run
+git-only with `provider = "off"`.
+
+| Provider | Status |
+|---|---|
+| GitHub | Supported |
+| Azure DevOps | Upcoming |
+| GitLab | Upcoming |
+| Forgejo | Upcoming |
+| Others | Under consideration |
+
+See the [Roadmap](../roadmap.md) for the broader picture.
diff --git a/docs/roadmap.md b/docs/roadmap.md
new file mode 100644
index 0000000..2162e63
--- /dev/null
+++ b/docs/roadmap.md
@@ -0,0 +1,34 @@
+# Roadmap
+
+WhyGraph works today for the core loop - scan a repo, serve evidence and rationale over MCP. Here's
+what's planned but not yet built. Treat everything below as direction, not a promise of dates.
+
+## More source-control providers
+
+GitHub is the only supported remote today. These are on the way:
+
+| Provider | Status |
+|---|---|
+| GitHub | Supported |
+| Azure DevOps | Upcoming |
+| GitLab | Upcoming |
+| Forgejo | Upcoming |
+| Others | Under consideration |
+
+Until then, run against a GitHub remote or stay git-only with `[scan].provider = "off"`. See
+[Providers](reference/providers.md).
+
+## Deferred capabilities
+
+Larger, net-new pieces that aren't built yet:
+
+- **Cross-repo project registry** - orchestrate WhyGraph across several repos from one place.
+- **Persistent / server mode** - a long-running endpoint with an HTTP MCP transport, so an app
+ doesn't spawn a fresh stdio session per connection. This is what unlocks the full
+ [service model](deploy/service.md).
+- **Per-branch databases** - separate CodeGraph and WhyGraph databases per branch, so a scan on one
+ branch doesn't clobber another's.
+
+!!! info "Want to weigh in?"
+ These are shaped by what people actually need. Open an issue on
+ [GitHub](https://github.com/mtrdesign/whygraph) if one of these matters to you.
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css
new file mode 100644
index 0000000..ab309d3
--- /dev/null
+++ b/docs/stylesheets/extra.css
@@ -0,0 +1,4 @@
+/* WhyGraph docs - brand-tuning hook.
+ *
+ * Intentionally near-empty. Material's indigo defaults carry the site for now;
+ * drop palette / typography overrides here when a brand identity lands. */
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 0000000..f492822
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,99 @@
+site_name: WhyGraph
+site_description: Rationale layer over CodeGraph — explains why code exists, not just what it does.
+site_url: https://mtrdesign.github.io/whygraph/ # project-pages subpath (also drives social cards)
+repo_url: https://github.com/mtrdesign/whygraph
+repo_name: mtrdesign/whygraph
+edit_uri: edit/main/docs/
+copyright: Copyright © MTR Design
+
+theme:
+ name: material
+ language: en
+ icon:
+ repo: fontawesome/brands/github
+ logo: material/graph-outline # built-in icon as logo until a brand asset exists
+ features:
+ - navigation.tabs # top-level sections as tabs
+ - navigation.tabs.sticky # tabs stay pinned on scroll
+ - navigation.sections # group pages in the sidebar
+ - navigation.indexes # section landing pages (the section title is itself a page)
+ - navigation.top # back-to-top button
+ - navigation.instant # SPA-like instant nav
+ - navigation.instant.progress # top loading bar on navigation
+ - navigation.tracking # URL tracks the scrolled-to anchor
+ - navigation.footer # prev/next footer links
+ - toc.follow
+ - search.suggest
+ - search.highlight
+ - content.code.copy # copy button on code blocks
+ - content.code.annotate # annotated code blocks
+ - content.tabs.link # linked content tabs (install variants, agents)
+ - content.tooltips # rich hover tooltips
+ - announce.dismiss # dismissible announcement bar
+ palette: # light/dark toggle
+ - media: "(prefers-color-scheme: light)"
+ scheme: default
+ primary: indigo
+ accent: indigo
+ toggle: { icon: material/brightness-7, name: Switch to dark mode }
+ - media: "(prefers-color-scheme: dark)"
+ scheme: slate
+ primary: indigo
+ accent: indigo
+ toggle: { icon: material/brightness-4, name: Switch to light mode }
+
+extra_css:
+ - stylesheets/extra.css # near-empty hook for future brand tuning
+
+markdown_extensions:
+ - admonition # note/warning/tip callouts
+ - attr_list # required for grid-card homepage
+ - md_in_html # required for grid-card homepage
+ - tables
+ - toc: { permalink: true }
+ - pymdownx.highlight: { anchor_linenums: true }
+ - pymdownx.inlinehilite
+ - pymdownx.snippets
+ - pymdownx.superfences: # required for mermaid diagrams
+ custom_fences:
+ - name: mermaid
+ class: mermaid
+ format: !!python/name:pymdownx.superfences.fence_code_format
+ - pymdownx.tabbed: { alternate_style: true } # tabbed install/agent variants
+ - pymdownx.details
+ - pymdownx.emoji:
+ emoji_index: !!python/name:material.extensions.emoji.twemoji
+ emoji_generator: !!python/name:material.extensions.emoji.to_svg
+
+plugins:
+ - search
+ - social: # Open Graph link-preview cards
+ cards: !ENV [CI, false] # generate only in CI (needs Cairo/Pango); skip locally
+ - git-revision-date-localized: # per-page "last updated" dates
+ enable_creation_date: true
+ type: timeago
+ fallback_to_build_date: true # don't fail --strict on uncommitted pages
+
+nav:
+ - Home: index.md
+ - Getting Started:
+ - getting-started/index.md
+ - Installation: getting-started/installation.md
+ - Quickstart: getting-started/quickstart.md
+ - User Guide:
+ - guide/index.md
+ - Concepts: guide/concepts.md
+ - Scanning your repo: guide/scanning.md
+ - Wiring your editor: guide/editors.md
+ - Using WhyGraph (MCP): guide/mcp-usage.md
+ - Docker & Self-Hosting:
+ - deploy/index.md
+ - Run with Docker: deploy/docker.md
+ - WhyGraph as a service: deploy/service.md
+ - Reference:
+ - reference/index.md
+ - CLI: reference/cli.md
+ - MCP surface: reference/mcp.md
+ - Configuration: reference/configuration.md
+ - Source control providers: reference/providers.md
+ - Roadmap: roadmap.md
diff --git a/pyproject.toml b/pyproject.toml
index 69ff2d2..a9e4a57 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,3 +36,7 @@ line-length = 88
[dependency-groups]
dev = ["pytest>=8", "ruff>=0.8"]
+docs = [
+ "mkdocs-material[imaging]>=9.5", # [imaging] → cairosvg + pillow for social cards
+ "mkdocs-git-revision-date-localized-plugin>=1.2", # per-page "last updated" dates
+]
diff --git a/uv.lock b/uv.lock
index a6d7ba1..d91154f 100644
--- a/uv.lock
+++ b/uv.lock
@@ -75,6 +75,56 @@ wheels = [
{ url = "https://files.pythonhosted.org/packages/64/b4/17d4b0b2a2dc85a6df63d1157e028ed19f90d4cd97c36717afef2bc2f395/attrs-26.1.0-py3-none-any.whl", hash = "sha256:c647aa4a12dfbad9333ca4e71fe62ddc36f4e63b2d260a37a8b83d2f043ac309", size = 67548, upload-time = "2026-03-19T14:22:23.645Z" },
]
+[[package]]
+name = "babel"
+version = "2.18.0"
+source = { registry = "https://pypi.org/simple" }
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