feat: Enable multi-codebase support with project-relative storage

## Problem: Hardcoded Paths Breaking Multi-Codebase Support

Previously, all CodeGraph indexes and databases used hardcoded `.codegraph`
paths relative to current working directory. This broke when:
- Indexing multiple projects (each needs isolated storage)
- Running MCP server from different directory than project root
- Managing multiple codebases simultaneously

## Solution: Project-Relative Storage Architecture

### Core Changes

**1. IndexerConfig Enhancement**
- Added `project_root: PathBuf` field
- Explicitly tracks which project is being indexed
- Defaults to current directory for backward compatibility

**2. ProjectIndexer Updates**
- Added `project_root` field to store project location
- Updated `new()` to use `CodeGraph::new_with_path(project_root/.codegraph/db)`
- All storage operations now use `self.project_root`:
  - FAISS indexes: `project_root/.codegraph/faiss.index`
  - Embeddings: `project_root/.codegraph/embeddings.json`
  - Metadata: `project_root/.codegraph/index.json`
  - Shards: `project_root/.codegraph/shards/{lang,path}/`

**3. CLI Improvements**
- `handle_index()`: Sets `project_root` from path parameter
- Clean command: Uses project-relative `.codegraph` directory
- Benchmark command: Uses project-relative paths
- Proper canonicalization of project paths

### Multi-Codebase Workflow

**Index multiple projects (isolated storage):**
```bash
codegraph index /home/user/project-a  # → /home/user/project-a/.codegraph/
codegraph index /home/user/project-b  # → /home/user/project-b/.codegraph/
codegraph index /opt/services/api     # → /opt/services/api/.codegraph/
```

**Serve different projects:**
```bash
# Terminal 1
cd /home/user/project-a && codegraph start stdio

# Terminal 2
cd /home/user/project-b && codegraph start stdio
```

**Claude Desktop multi-project config:**
```json
{
  "mcpServers": {
    "codegraph-api": {
      "command": "codegraph",
      "args": ["start", "stdio"],
      "cwd": "/opt/services/api"
    },
    "codegraph-frontend": {
      "command": "codegraph",
      "args": ["start", "stdio"],
      "cwd": "/opt/services/frontend"
    }
  }
}
```

### Directory Structure (Each Project Isolated)

```
project-a/
├── src/
├── .codegraph/              # Project A's index
│   ├── db/                  # RocksDB (isolated)
│   ├── faiss.index          # FAISS index (isolated)
│   ├── faiss_ids.json
│   ├── shards/
│   │   ├── lang/
│   │   └── path/
│   └── index.json

project-b/
├── app/
├── .codegraph/              # Project B's index (completely separate)
│   ├── db/                  # Different RocksDB instance
│   ├── faiss.index          # Different FAISS index
│   └── ...
```

## Protocol Compliance

### MCP Official SDK
- Uses official `rmcp` framework
- Proper tool schemas with `JsonSchema` derive
- Standard error codes (-32602 invalid params, -32603 internal error)
- STDIO transport (official MCP protocol)

### Error Handling
```rust
if query.is_empty() {
    return Err(McpError {
        code: -32602,
        message: "Query cannot be empty".to_string(),
        data: None,
    });
}
```

### Tool Registration
- `#[tool_router]` macro for automatic registration
- `#[tool(description = "...")]` for each tool
- `Parameters<T>` wrapper for type-safe parameter parsing

## Performance Features

**1. Read-Only Fallback**
- MCP server gracefully falls back to read-only mode
- Allows multiple servers to read same index
- No RocksDB lock conflicts

**2. Sharded FAISS Indexes**
- Language shards: Search only Rust/TypeScript/Python/etc
- Path shards: Search only src/lib/tests/etc
- Faster queries by filtering before FAISS search

**3. Batch Embedding** (from Phase 1)
- 10-50x speedup from batched GPU processing

## Benefits

✅ **Multi-Codebase**: Each project has isolated `.codegraph/` storage
✅ **No Cross-Contamination**: Clear project boundaries
✅ **Scalability**: Run multiple MCP servers (one per project)
✅ **Protocol Compliant**: Uses official `rmcp` SDK
✅ **Performance**: Sharded indexes, batch processing, read-only mode
✅ **Developer Experience**: Simple `cd project && codegraph index .`

## Files Modified

- `crates/codegraph-mcp/src/indexer.rs`
  - Added `project_root` to `IndexerConfig` and `ProjectIndexer`
  - Updated all `.codegraph` paths to use `self.project_root`
  - Fixed metadata/embedding paths to be project-relative

- `crates/codegraph-mcp/src/bin/codegraph.rs`
  - Set `project_root` from path parameter in index command
  - Fixed clean command to use project-relative paths
  - Updated benchmark to use project-relative paths

- `MCP_IMPROVEMENTS.md`
  - Comprehensive documentation of multi-codebase architecture
  - Protocol compliance details
  - Migration guide and testing scenarios

## Migration

**Existing users**: Re-index to ensure proper structure
```bash
cd /path/to/project && codegraph index . --force
```

**New users**: Just works automatically
```bash
cd /path/to/project && codegraph index .
```

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: claude