# Story 9.1: Comprehensive Project Documentation

Status: done

<!-- Note: Validation is optional. Run validate-create-story for quality check before dev-story. -->

## Story

As a Technical Writer / Developer,
I want to build comprehensive project documentation in the docs folder and update the root README.md,
so that users and developers have clear guidance, and AI agents can maintain the documentation effectively.

## Acceptance Criteria

1. **Given** the current project state, **when** the documentation is built, **then** a `docs/` folder is created containing comprehensive documentation.
2. **Given** the `docs/` folder, **then** it must contain:
    - **Overview & Motivation**: Why lucius-mcp exists and its core mission.
    - **Architecture & Design**: Detailed explanation of the "Thin Tool / Fat Service" pattern, "Agent Hints", and project structure.
    - **Tool Reference**: Complete list of all MCP tools with their purpose, parameters, and examples.
    - **Configuration & Setup**: Comprehensive guide for environment variables, MCP modes (stdio/http), and installation.
    - **Development Guide**: Instructions for adding new tools, services, and regenerating the API client.
3. **Given** the root `README.md`, **then** it must be updated to contain:
    - Short introduction.
    - Project motivation (why lucius-mcp).
    - **Supported Tools Table** (Brief table with tool name and short description).
    - Quick start guide with link to more thorough instructions.
    - Documentation section (link to `docs/` and short introduction).
    - Contributing section (short message and link to contribution guidelines).
4. **Given** the documentation, **then** it must include a comprehensive scenario/protocol for AI agents to update this documentation in the future when new features or tools are added.
5. All documentation MUST be written in Markdown and follow the project's formatting standards.

## Tasks / Subtasks

- [x] **Task 1: Initialize Documentation Structure** (AC: #1, #2)
    - [x] 1.1: Create `docs/` directory.
    - [x] 1.2: Create `docs/index.md` (Overview & Motivation).
- [x] **Task 2: Document Architecture and Design** (AC: #2)
    - [x] 2.1: Create `docs/architecture.md`.
    - [x] 2.2: Document project structure, Thin Tool / Fat Service pattern, and Agent Hint system.
- [x] **Task 3: Document MCP Tools** (AC: #2)
    - [x] 3.1: Create `docs/tools.md`.
    - [x] 3.2: Iterate through all files in `src/tools/` and document each tool.
- [x] **Task 4: Document Configuration and Setup** (AC: #2)
    - [x] 4.1: Create `docs/setup.md`.
    - [x] 4.2: Document environment variables, stdio vs http modes, and Claude Desktop installation.
- [x] **Task 5: Document Development Guide** (AC: #2)
    - [x] 5.1: Create `docs/development.md`.
    - [x] 5.2: Document adding tools/services and API client regeneration.
- [x] **Task 6: Implement AI Agent Update Protocol** (AC: #4)
    - [x] 6.1: Create `docs/agent-documentation-protocol.md` with a scenario for future updates.
- [x] **Task 7: Update Root README.md** (AC: #3)
    - [x] 7.1: Refactor root `README.md` according to the specified structure.

## Dev Notes

### Architecture Compliance (CRITICAL)

- Use the existing implementation artifacts in `specs/implementation-artifacts/` as the primary source of truth for features and history.
- Ensure the "Agent Hint" philosophy is reflected in the documentation (tools are for agents).
- The "Thin Tool / Fat Service" pattern must be clearly explained to maintain codebase quality.

### Project Structure Notes

- Alignment with unified project structure: `src/tools`, `src/services`, `src/client`.
- Naming conventions: snake_case for tools, CamelCase for DTOs.

### References

- [Source: specs/implementation-artifacts/1-1-project-initialization-and-core-architecture.md]
- [Source: specs/implementation-artifacts/3-11-crud-custom-field-values.md] (and other tool-related artifacts)
- [Source: pyproject.toml]

## Dev Agent Record

### Agent Model Used

Google DeepMind Antigravity

### Debug Log References

### Completion Notes List

- Built comprehensive documentation suite in `docs/`.
- Implemented link validation tests in `tests/docs/test_doc_links.py`.
- Added `scripts/update-changelog.md` for standardized versioning documentation.
- Polished README.md with comprehensive tool table and agent-friendly sections.

### File List

- [README.md](file:///Users/anmaro/Code/personal/github.com/lucius-mcp/README.md)
- [CONTRIBUTING.md](file:///Users/anmaro/Code/personal/github.com/lucius-mcp/CONTRIBUTING.md)
- [docs/index.md](file:///Users/anmaro/Code/personal/github.com/lucius-mcp/docs/index.md)
- [docs/architecture.md](file:///Users/anmaro/Code/personal/github.com/lucius-mcp/docs/architecture.md)
- [docs/tools.md](file:///Users/anmaro/Code/personal/github.com/lucius-mcp/docs/tools.md)
- [docs/setup.md](file:///Users/anmaro/Code/personal/github.com/lucius-mcp/docs/setup.md)
- [docs/development.md](file:///Users/anmaro/Code/personal/github.com/lucius-mcp/docs/development.md)
- [docs/agent-documentation-protocol.md](file:///Users/anmaro/Code/personal/github.com/lucius-mcp/docs/agent-documentation-protocol.md)
- [tests/docs/test_doc_links.py](file:///Users/anmaro/Code/personal/github.com/lucius-mcp/tests/docs/test_doc_links.py)
- [scripts/update-changelog.md](file:///Users/anmaro/Code/personal/github.com/lucius-mcp/scripts/update-changelog.md)
