Remove Docker, update README with setup and auto-start instructions

- Remove Dockerfile and docker-compose.yaml (not suitable for this project)
- Update README.md with comprehensive setup documentation
- Add systemd, tmux, and rc.local auto-start options
- Add troubleshooting section
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# Knowledge Base
# Knowledge Base RAG System
Personal knowledge base repository for storing useful information, notes, and documentation.
A self-hosted RAG (Retrieval Augmented Generation) system for your Obsidian vault with MCP server integration.
## Contents
## Features
- [Getting Started](#getting-started)
- [Contributing](#contributing)
- [License](#license)
- **Semantic Search**: Find relevant content using embeddings, not just keywords
- **MCP Server**: Exposes search, indexing, and stats tools via MCP protocol
- **Local-first**: No external APIs - everything runs locally
- **Obsidian Compatible**: Works with your existing markdown vault
## Getting Started
## Requirements
This repository contains various knowledge articles, how-to guides, and reference documentation.
- Python 3.11+
- ~2GB disk space for embeddings model
## Contributing
## Quick Start
Feel free to contribute by creating issues or submitting pull requests.
### 1. Install uv (if not already)
```bash
curl -LsSf https://astral.sh/uv/install.sh | sh
source ~/.local/bin/env
```
### 2. Clone and setup
```bash
cd ~/knowledge-base
cp .env.example .env
```
### 3. Configure
Edit `.env` to set your vault path:
```bash
VAULT_PATH=/path/to/your/obsidian-vault
EMBEDDING_MODEL=all-MiniLM-L6-v2 # optional
```
### 4. Install dependencies
```bash
uv sync
```
### 5. Run the server
```bash
source .venv/bin/activate
VAULT_PATH=./knowledge python -m knowledge_rag.server
```
The server will:
- Auto-index your vault on startup
- Listen for MCP requests via stdio
## MCP Tools
Once running, these tools are available:
| Tool | Description |
|------|-------------|
| `search_knowledge` | Semantic search across your vault |
| `index_knowledge` | Re-index the vault (use after adding files) |
| `get_knowledge_stats` | View indexing statistics |
## Usage Example
```python
# Example: Searching the knowledge base
# (via MCP client or Claude Desktop integration)
await search_knowledge({
"query": "how does the RAG system work",
"top_k": 5
})
```
## Auto-Start on Boot
### Option 1: Systemd Service
Create `/etc/systemd/system/knowledge-rag.service`:
```ini
[Unit]
Description=Knowledge Base RAG MCP Server
After=network.target
[Service]
Type=simple
User=ernie
WorkingDirectory=/home/ernie/knowledge-base
Environment="VAULT_PATH=/home/ernie/knowledge"
Environment="PATH=/home/ernie/.local/bin:/usr/bin:/bin"
ExecStart=/home/ernie/knowledge-base/.venv/bin/python -m knowledge_rag.server
Restart=always
[Install]
WantedBy=multi-user.target
```
Then enable:
```bash
sudo systemctl daemon-reload
sudo systemctl enable knowledge-rag.service
sudo systemctl start knowledge-rag.service
```
### Option 2: tmux/screen
```bash
# Start in tmux
tmux new -s knowledge-rag
source .venv/bin/activate
VAULT_PATH=./knowledge python -m knowledge_rag.server
# Detach: Ctrl+b, then d
```
### Option 3: rc.local or startup script
Add to your `~/.bashrc` or startup script:
```bash
# Only start if not already running
if ! pgrep -f "knowledge_rag.server" > /dev/null; then
cd ~/knowledge-base
source .venv/bin/activate
VAULT_PATH=./knowledge nohup python -m knowledge_rag.server > /tmp/knowledge-rag.log 2>&1 &
fi
```
## Project Structure
```
knowledge-base/
├── src/knowledge_rag/ # Source code
│ ├── server.py # MCP server
│ ├── chunker.py # Markdown chunking
│ ├── embeddings.py # Sentence-transformers wrapper
│ └── vector_store.py # ChromaDB wrapper
├── knowledge/ # Your Obsidian vault (gitignored)
├── pyproject.toml # Project config
└── .env.example # Environment template
```
## Configuration
| Variable | Default | Description |
|----------|---------|-------------|
| `VAULT_PATH` | `/data/vault` | Path to your Obsidian vault |
| `EMBEDDING_MODEL` | `all-MiniLM-L6-v2` | Sentence-transformers model |
| `EMBEDDINGS_CACHE_DIR` | `/data/embeddings_cache` | Model cache location |
## Troubleshooting
### First run is slow
The embedding model (~90MB) downloads on first run. Subsequent runs are faster.
### No search results
Run `index_knowledge` tool to index your vault, or restart the server.
### Out of memory
The default model is lightweight. For even smaller models, try `paraphrase-MiniLM-L3-v2`.
## License
MIT License
MIT