DocForge2/docs/USER_MANUAL.md

# DocForge user manual

DocForge turns project-owned documentation and source projections into a validated graph that
people and AI agents can search, inspect, visualize, and change through reviewable proposals.
Canonical project files remain authoritative. The SQLite graph, previews, rendered manuals, and
viewer processes are derived and can be rebuilt.

## Features

- Project-bound Markdown and TOML documentation graphs with stable node IDs.
- Deterministic validation for metadata, relationships, dependency cycles, paths, and limits.
- Disposable SQLite indexing with lexical search, filters, backlinks, dependencies, and impact.
- Bounded context profiles for AI agents, including source paths and content hashes.
- Isolated, optimistic changesets with create, update, move, delete, validation, diffs, and previews.
- Hash-bound canonical application through both CLI and an explicitly enabled MCP tool.
- Declared HTML render views. Arbitrary templates, render commands, and output paths are rejected.
- A loopback-only graph browser with Nodes and Flow views, relationship keys, source inspection,
  node hiding, panel resizing, zooming, and managed idle shutdown.
- A generic Markdown/TOML adapter plus contracts for deterministic project-owned adapters.

DocForge does not run shell commands from documentation, mutate Git, build an application, deploy,
publish, choose a project globally, or cross project boundaries.

## Mental model

One `.docforge/project.toml` binds DocForge to one project root. The descriptor declares canonical
content roots, authority files, derived paths, proposal writers, relationship types, limits,
context profiles, and optional render views.

Canonical files own facts:

```text
canonical Markdown/TOML or adapter sources
    ↓ validate
disposable SQLite graph
    ↓ query / visualize / compile context
people and agents
    ↓ propose
isolated changeset + preview
    ↓ exact hash approval
canonical apply
    ↓
reindexed graph + declared renders
```

An apply operation is deliberately narrower than a general file editor. It accepts one validated
changeset ID and the exact SHA-256 changeset hash that was reviewed. It rejects stale canonical
sources, changed proposals, overlapping proposals, unauthorized families or operations, unsafe
paths, symlink escapes, and projections that do not round-trip through the project loader.

The generic adapter can serialize its Markdown and TOML nodes directly. A custom adapter must
provide its own canonical applier because only that project knows how a graph node maps back to its
source format.

## Setup

### Requirements

- Python 3.12 or newer.
- [`uv`](https://docs.astral.sh/uv/) for the development environment.
- Node.js and npm for browser asset validation and strict Pyright checking.

Clone and verify DocForge:

```bash
git clone forgejo@repo.andraxion.net:administrator/DocForge.git /absolute/path/DocForge
cd /absolute/path/DocForge
uv sync --group dev
npm ci

npx pyright
npm run lint:web
uv run ruff check src tests tools
uv run ruff format --check src tests tools
uv run pytest -q
```

Use the executables under `/absolute/path/DocForge/.venv/bin/` when DocForge is not installed into
the active shell environment.

### Configure a generic project

Create `/absolute/path/MyProject/.docforge/project.toml`:

```toml
schema_version = 1
project_id = "my-project"
title = "My Project"
adapter = "generic"

[sources]
content_roots = ["Docs/Manual"]
authority_files = []

[derived]
cache_root = ".docforge/cache"
index = ".docforge/cache/index.sqlite3"

[changesets]
root = ".docforge/changesets"

[[changesets.writers]]
id = "project-editor"
families = ["architecture", "system", "operations", "roadmap"]
operations = ["create", "update", "move", "delete"]

[render]
template_root = "Docs/Templates"
preview_root = ".docforge/previews"

[[render.views]]
id = "manual"
renderer = "generic_html"
template = "manual.html"
output = "Docs/Rendered/Manual.html"
title = "My Project Manual"
families = ["architecture", "system", "operations", "roadmap"]

[graph]
allowed_relations = ["depends_on", "owns", "calls", "reads", "writes", "tested_by", "relates_to"]

[limits]
max_source_bytes = 500000
max_nodes = 10000
max_query_chars = 500
max_results = 100
max_traversal_depth = 6
max_context_tokens = 12000
max_changesets = 100
max_changeset_operations = 100
max_changeset_bytes = 1000000

[[profiles]]
id = "development"
families = ["architecture", "system", "operations", "roadmap"]
statuses = ["current", "active", "verified"]
required_nodes = ["architecture.overview"]
token_budget = 8000
dependency_depth = 3
```

Every path is resolved against the explicit project root. Canonical content, derived cache, and
changeset roots must not overlap.

### Add a Markdown node

Create `Docs/Manual/architecture-overview.md`:

```markdown
+++
schema_version = 1
id = "architecture.overview"
title = "Architecture overview"
family = "architecture"
authority = "authoritative"
status = "current"
tags = ["architecture", "ownership"]
summary = "Defines the top-level systems and ownership boundaries."
depends_on = ["system.persistence"]
+++

# Architecture overview

Describe the project’s systems, authorities, persistence owners, runtime flow, failure behavior,
tests, and operational entry points.
```

Each Markdown file contains one node. A TOML source may contain multiple `[[nodes]]` records. TOML
nodes need stable `source_anchor` values when proposals may create or move records within the file.
Every relationship target must exist.

### Build the graph

```bash
PROJECT=/absolute/path/MyProject
DOCFORGE=/absolute/path/DocForge/.venv/bin/docforge

"$DOCFORGE" --project-root "$PROJECT" validate
"$DOCFORGE" --project-root "$PROJECT" reindex
"$DOCFORGE" --project-root "$PROJECT" context development
```

`reindex` builds the SQLite graph and immediately checks its identity. Run it after canonical
documentation or adapter sources change.

### Install the viewer manager

Install the native per-user supervisor once:

```bash
docforge-viewer-manager install-user-service
```

Linux uses `systemd --user`, macOS uses a LaunchAgent, and Windows uses Task Scheduler. If the
virtual environment moves, reinstall the service so it points at the current Python interpreter.

For a temporary foreground manager:

```bash
docforge-viewer-manager serve
```

Open a project graph without Codex:

```bash
docforge --project-root "$PROJECT" visualize
docforge --project-root "$PROJECT" visualize --node architecture.overview
docforge --project-root "$PROJECT" visualize --query persistence
```

The command opens the default browser. Add `--no-open` when a script only needs the returned JSON
URL. Use `visualization-status` and `visualization-stop` to inspect or stop the project viewer.

## Visualization usage

- Left-click a node for its compact descriptor.
- Right-click a node for the full inspector.
- Use **Open source** to read the node’s project-confined source at its anchor.
- Use **Hide node** to remove noisy non-focus nodes from the current presentation.
- Use **Restore hidden** above the graph to bring hidden nodes back.
- Use **Explore neighborhood** to make a node the new focus.
- Switch to **Flow** to inspect bounded directed ancestry.
- Use the mouse wheel or viewport buttons to zoom. Drag the canvas to pan. Press Space to center
  the selected node.

Hidden nodes are a browser presentation preference. They do not alter the index or canonical graph.
The focus node cannot be hidden; focus another node first.

Source navigation depends on adapter evidence. Numeric anchors, line-style anchors such as `L120`,
TOML `node-N` anchors, heading slugs, and searchable text anchors are recognized. If a custom
adapter supplies only a path or a vague symbol, the source viewer opens the file and falls back to
the closest match or first line.

## CLI usage

Every command emits deterministic JSON:

```bash
docforge --project-root /absolute/path/MyProject <command>
```

### Project and index commands

```text
info
validate
build
reindex
check
validate-index
```

- `info` reports the project binding and index health.
- `validate` validates current canonical sources without requiring an index.
- `build` rebuilds the disposable index.
- `reindex` rebuilds and checks the index in one operation.
- `check` and `validate-index` verify that the existing index matches current sources.

### Query commands

```text
show NODE_ID
search QUERY [--limit N]
filter [--family X] [--authority X] [--status X] [--tag X] [--limit N]
backlinks NODE_ID [--relation RELATION]
dependencies NODE_ID [--depth N]
impact NODE_ID [--depth N]
context PROFILE [--budget N]
```

### Render and proposal commands

```text
render-status [VIEW_ID]
render VIEW_ID
preview CHANGESET_ID VIEW_ID
apply CHANGESET_ID --changeset-hash SHA256 --applier WRITER_ID
```

The CLI apply command supports the generic adapter. It verifies that the configured writer owns the
changeset, applies the exact reviewed hash, rebuilds the index, checks it, and regenerates every
declared render. It does not commit or push the result.

### Viewer commands

```text
visualize [--node NODE_ID | --query QUERY] [--depth N] [--no-open]
visualization-status
visualization-stop
```

## MCP usage

Run one MCP server per project with absolute paths:

```bash
docforge-mcp \
  --project-root /absolute/path/MyProject \
  --proposal-writer project-editor
```

Omit `--proposal-writer` when the MCP client should not create or append proposals.

To expose canonical application, add a separate explicit startup gate:

```bash
docforge-mcp \
  --project-root /absolute/path/MyProject \
  --proposal-writer project-editor \
  --canonical-applier project-editor
```

Without `--canonical-applier`, `docforge_apply_changeset` is not registered. The flag is an
identity, not a command. The changeset creator, configured writer, and canonical applier must agree.

Example MCP client configuration:

```json
{
  "mcpServers": {
    "my-project-docforge": {
      "command": "/absolute/path/DocForge/.venv/bin/docforge-mcp",
      "args": [
        "--project-root",
        "/absolute/path/MyProject",
        "--proposal-writer",
        "project-editor",
        "--canonical-applier",
        "project-editor"
      ]
    }
  }
}
```

### Read tools

- `docforge_project_info`
- `docforge_get_contract`
- `docforge_get_node`
- `docforge_search`
- `docforge_filter_nodes`
- `docforge_backlinks`
- `docforge_dependencies`
- `docforge_impact`
- `docforge_get_context`
- `docforge_validate_project`
- `docforge_render_status`
- `docforge_visualize`
- `docforge_visualization_status`
- `docforge_stop_visualization`

### Proposal tools

- `docforge_create_changeset`
- `docforge_list_changesets`
- `docforge_get_changeset`
- `docforge_propose_node_create`
- `docforge_propose_node_update`
- `docforge_propose_node_move`
- `docforge_propose_node_delete`
- `docforge_validate_changeset`
- `docforge_get_changeset_diff`
- `docforge_preview_changeset`

### Application tool

- `docforge_apply_changeset`

The application call requires `changeset_id` and `expected_changeset_hash`. Always retrieve and
inspect the final diff after the last proposal mutation. Apply that exact hash. A proposal mutation
creates a new hash, so an earlier approval cannot silently apply later content.

Recommended agent sequence:

1. Read the contract and relevant nodes.
2. Create a changeset.
3. Add structured operations using the hash returned by each previous mutation.
4. Validate the changeset.
5. Inspect its structured diff and preview.
6. Obtain human approval for the final changeset hash when required by the client workflow.
7. Call `docforge_apply_changeset` with that exact hash.
8. Report changed canonical files and derived refresh results.

Custom adapters may expose the application tool only when they supply a project-owned
`CanonicalApplier`. Core DocForge will not guess how adapter nodes map back to canonical sources.

## Troubleshooting

### `stale_index` or `visualization_stale`

Canonical sources changed after the index or viewer snapshot was built.

```bash
docforge --project-root "$PROJECT" reindex
docforge --project-root "$PROJECT" visualize
```

An existing graph browser intentionally stays pinned to its original index identity. Reopen it
after reindexing.

### `visualization_manager_unavailable`

The per-user manager is not installed, is stopped, or points to an old virtual environment.

```bash
docforge-viewer-manager install-user-service
```

For diagnosis, run `docforge-viewer-manager serve` in a terminal and retry `docforge visualize`.

### The browser did not open

The command still returns the loopback URL as JSON. Open that URL manually. Desktop-less sessions
should use `--no-open`. Confirm a local browser is registered as the default URL handler.

### `docforge_apply_changeset` is missing

The MCP server was started without `--canonical-applier`, or a custom adapter did not supply a
canonical applier. Restart the MCP server with the explicit gate after deciding that canonical
application is appropriate for that project.

### `canonical_application_disabled`

The CLI/MCP process has no matching configured applier identity. Confirm the ID exists under
`[[changesets.writers]]`, owns the changeset, and is passed exactly to `--applier` or
`--canonical-applier`.

### `changeset_conflict`

The changeset changed after the caller read it. Retrieve the changeset and diff again. Review the
new hash rather than retrying with the old approval.

### `base_conflict`, `content_conflict`, or `proposal_conflict`

- `base_conflict`: canonical sources changed after changeset creation.
- `content_conflict`: a target node no longer has the expected content hash.
- `proposal_conflict`: another active proposal from the same base touches the same node or source.

Do not force apply. Rebase the intended changes into a new changeset after inspecting current
canonical content.

### `application_mismatch`

The written sources did not reproduce the validated projection. DocForge rolls the generic
canonical files back. For a custom adapter, fix its serializer or node-to-source mapping before
retrying.

### `path_escape`, `unsafe_template`, or missing source

DocForge rejects absolute paths, parent traversal, symlink escapes, overlapping canonical and
derived roots, unsafe render outputs, and source files outside the project root. Fix the descriptor
or adapter projection. Do not weaken confinement to make the error disappear.

### Source opens at the wrong place

The source path comes from the node. The anchor comes from the generic source or custom adapter.
Improve the adapter’s `source_anchor` to a line, stable heading, TOML `node-N` anchor, or distinctive
symbol. DocForge can open the file safely, but it cannot infer a perfect code location from
ambiguous adapter evidence.

### Full inspector content does not fit

DocForge 0.13 uses a fixed header and footer with a scrollable inspector body. If an older page is
still open, stop and reopen the visualization so it loads the current `graph-browser@12` template.

### Render output is stale

```bash
docforge --project-root "$PROJECT" render-status
docforge --project-root "$PROJECT" render VIEW_ID
```

Successful canonical apply regenerates all declared views automatically. A manual canonical edit
requires reindexing and rendering.

### Descriptor changed after startup

Long-lived CLI/MCP bindings fail closed if `.docforge/project.toml` changes underneath them. Restart
the process so it binds the new descriptor deliberately.

## Development and verification

Run the complete release gate from the DocForge repository:

```bash
npx pyright
npm run lint:web
uv run ruff check src tests tools
uv run ruff format --check src tests tools
uv run python -m compileall -q src tests tools
uv run pytest -q
```

Project-specific vocabulary, extraction rules, and serialization belong in the project adapter.
Generic core behavior must remain deterministic, project-bound, and recoverable.