@ncukondo/reference-manager 0.1.0 → 0.4.0

package/README.md

@@ -1,17 +1,72 @@
 # reference-manager
 
-A local reference management tool using CSL-JSON as the single source of truth.
+> Automate your literature workflow — from systematic reviews to manuscript writing
 
-## Features
+[![npm version](https://img.shields.io/npm/v/@ncukondo/reference-manager.svg)](https://www.npmjs.com/package/@ncukondo/reference-manager)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Status: Alpha](https://img.shields.io/badge/Status-Alpha-orange.svg)]()
 
-- **CSL-JSON Native**: Uses CSL-JSON format as the primary data model
-- **Command-line Interface**: Comprehensive CLI with search, add, update, remove commands
-- **HTTP Server**: Optional background server for improved performance
-- **Duplicate Detection**: Automatic detection via DOI, PMID, or title+author+year
-- **Smart Search**: Full-text search with field-specific queries
-- **File Monitoring**: Automatic reload on external changes
-- **Backup Management**: Automatic backups with retention policies
-- **Pandoc Compatible**: Works seamlessly with Pandoc's bibliography system
+A command-line reference management tool designed for automation. Integrates with AI agents (Claude Code, Claude Desktop) via MCP and works seamlessly with shell scripts and Pandoc.
+
+## Why reference-manager?
+
+Traditional reference managers (Zotero, Mendeley, EndNote) are designed for manual, GUI-based workflows. **reference-manager** takes a different approach:
+
+- **Automation-first**: Every operation is available via CLI and MCP — no GUI required
+- **AI-native**: Direct integration with Claude and other AI agents through the Model Context Protocol
+- **Single source of truth**: CSL-JSON format ensures compatibility and transparency
+- **Pandoc-ready**: Generate citations in any style, ready for academic writing
+
+## Use Cases
+
+### Systematic Review / Scoping Review
+
+Automate the tedious parts of literature reviews:
+
+```bash
+# Import references from multiple sources
+ref add pmid:12345678 pmid:23456789
+ref add "10.1234/example.doi"
+ref add exported-from-pubmed.nbib
+
+# AI-assisted screening (with Claude Code)
+# "Review the abstracts in my library and flag potentially relevant papers for my review on AI in medical education"
+
+# Export for analysis
+ref list --format json > references.json
+```
+
+### Manuscript Writing
+
+Streamline your writing workflow:
+
+```bash
+# Generate citations
+ref cite smith2024 jones2023 --style apa
+# Output: (Smith, 2024; Jones, 2023)
+
+# Attach and manage full-text PDFs
+ref fulltext attach smith2024 ~/papers/smith2024.pdf
+
+# Export for Pandoc
+ref list --format json > references.json
+pandoc manuscript.md --bibliography references.json -o manuscript.docx
+```
+
+### AI-Assisted Research
+
+Let Claude help manage your references:
+
+```
+You: "Find all papers by Smith published after 2020"
+Claude: [uses search tool] Found 3 references...
+
+You: "Generate an APA citation for the machine learning paper"
+Claude: [uses cite tool] Smith, J. (2024). Machine learning applications...
+
+You: "Add this paper: 10.1234/example"
+Claude: [uses add tool] Added reference: example2024
+```
 
 ## Installation
 
@@ -19,10 +74,10 @@ A local reference management tool using CSL-JSON as the single source of truth.
 
 - Node.js 22 or later
 
-### From npm (when published)
+### From npm
 
 ```bash
-npm install -g reference-manager
+npm install -g @ncukondo/reference-manager
 ```
 
 ### From source
@@ -35,59 +90,182 @@ npm run build
 npm link
 ```
 
-## Usage
+## Quick Start
+
+```bash
+# Initialize (creates default config and empty library)
+ref list
+
+# Add a reference by DOI
+ref add "10.1038/nature12373"
+
+# Add from PubMed
+ref add pmid:25056061
+
+# Search your library
+ref search "author:smith machine learning"
+
+# Generate a citation
+ref cite smith2024 --style apa
+
+# List all references
+ref list
+```
+
+## AI Integration (MCP)
+
+reference-manager provides an MCP (Model Context Protocol) server for direct integration with AI agents.
+
+### Claude Code Setup
+
+Add reference-manager as an MCP server (no global installation required):
+
+```bash
+claude mcp add reference-manager -- npx -y @ncukondo/reference-manager mcp
+```
+
+Or with a custom library path:
+
+```bash
+claude mcp add reference-manager -- npx -y @ncukondo/reference-manager mcp --library ~/my-references.json
+```
+
+### Claude Desktop Setup
+
+Add to your Claude Desktop configuration file:
+
+**macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json`
+**Windows**: `%APPDATA%\Claude\claude_desktop_config.json`
+
+```json
+{
+  "mcpServers": {
+    "reference-manager": {
+      "command": "npx",
+      "args": ["-y", "@ncukondo/reference-manager", "mcp"]
+    }
+  }
+}
+```
+
+With a custom library:
+
+```json
+{
+  "mcpServers": {
+    "reference-manager": {
+      "command": "npx",
+      "args": ["-y", "@ncukondo/reference-manager", "mcp", "--library", "/path/to/library.json"]
+    }
+  }
+}
+```
+
+### Available Tools
+
+| Tool | Description | Parameters |
+|------|-------------|------------|
+| `search` | Search references by query | `query`: Search string (e.g., `"author:smith 2024"`) |
+| `list` | List all references | `format?`: `"json"` \| `"bibtex"` \| `"pretty"` |
+| `add` | Add new reference(s) | `input`: DOI, PMID, BibTeX, RIS, or CSL-JSON |
+| `remove` | Remove a reference | `id`: Reference ID, `force`: must be `true` |
+| `cite` | Generate formatted citation | `ids`: Array of reference IDs, `style?`: Citation style, `format?`: `"text"` \| `"html"` |
+| `fulltext_attach` | Attach PDF/Markdown to reference | `id`: Reference ID, `path`: File path |
+| `fulltext_get` | Get full-text content | `id`: Reference ID |
+| `fulltext_detach` | Detach full-text from reference | `id`: Reference ID |
 
-The command `ref` is available after installation (alias: `reference-manager`).
+### Available Resources
+
+| URI | Description |
+|-----|-------------|
+| `library://references` | All references as CSL-JSON array |
+| `library://reference/{id}` | Single reference by ID |
+| `library://styles` | Available citation styles |
+
+## CLI Reference
 
 ### Basic Commands
 
 ```bash
 # List all references
 ref list
+ref list --format json
+ref list --format bibtex
 
 # Search references
-ref search "author:smith machine learning"
-
-# Add a new reference (from JSON file)
-ref add reference.json
+ref search "machine learning"
+ref search "author:smith"
+ref search "author:jones year:2024"
+ref search "title:\"deep learning\""
+
+# Add references
+ref add paper.json                    # From CSL-JSON file
+ref add references.bib                # From BibTeX
+ref add export.ris                    # From RIS
+ref add "10.1038/nature12373"         # From DOI
+ref add pmid:25056061                 # From PubMed ID
+cat references.json | ref add         # From stdin
 
-# Add from stdin
-cat reference.json | ref add
+# Remove a reference
+ref remove smith2024
+ref remove smith2024 --force          # Skip confirmation
 
 # Update a reference
-ref update smith-2020 updates.json
+ref update smith2024 updates.json
+ref update smith2024 --set "title=New Title"
 
-# Remove a reference
-ref remove smith-2020
+# Generate citations
+ref cite smith2024
+ref cite smith2024 jones2023 --style apa
+ref cite smith2024 --style chicago-author-date --format html
+```
 
-# Server management
-ref server start
-ref server status
-ref server stop
+### Fulltext Management
+
+```bash
+# Attach files
+ref fulltext attach smith2024 ~/papers/smith2024.pdf
+ref fulltext attach smith2024 ~/notes/smith2024.md
+ref fulltext attach smith2024 paper.pdf --move    # Move instead of copy
+ref fulltext attach smith2024 paper.pdf --force   # Overwrite existing
+
+# Get attached files
+ref fulltext get smith2024 --pdf                  # Get PDF path
+ref fulltext get smith2024 --md                   # Get Markdown path
+ref fulltext get smith2024 --pdf --stdout         # Output content to stdout
+
+# Detach files
+ref fulltext detach smith2024 --pdf
+ref fulltext detach smith2024 --pdf --delete      # Also delete the file
 ```
 
 ### Output Formats
 
-```bash
-# Pretty format (default)
-ref list
+| Format | Flag | Description |
+|--------|------|-------------|
+| Pretty | (default) | Human-readable format |
+| JSON | `--format json` | CSL-JSON array |
+| BibTeX | `--format bibtex` | BibTeX format |
+| IDs only | `--format ids-only` | One ID per line |
 
-# JSON format
-ref list --format json
+### Search Query Syntax
 
-# BibTeX format
-ref list --format bibtex
+- **Simple search**: `machine learning` (matches any field)
+- **Field-specific**: `author:smith`, `title:neural`, `year:2024`
+- **Phrase search**: `"machine learning"` (exact phrase)
+- **Combined**: `author:smith "deep learning" 2024`
 
-# IDs only
-ref list --format ids-only
-```
+Supported field prefixes: `author:`, `title:`, `doi:`, `pmid:`, `pmcid:`, `url:`, `keyword:`, `tag:`
 
-### Configuration
+## Configuration
 
-Configuration file: `.reference-manager.config.toml`
+Configuration file: `~/.reference-manager.config.toml`
 
 ```toml
+# Path to the library file
 library = "~/references.json"
+
+# Logging level: silent, info, debug
 log_level = "info"
 
 [backup]
@@ -95,73 +273,93 @@ enabled = true
 max_count = 10
 max_age_days = 30
 
+[fulltext]
+directory = "~/references/fulltext"
+
 [server]
 auto_start = true
 auto_stop_minutes = 60
 ```
 
-See `spec/architecture/cli.md` for full configuration options.
+### Environment Variables
 
-## Development
+| Variable | Description |
+|----------|-------------|
+| `REFERENCE_MANAGER_LIBRARY` | Override library file path |
+| `REFERENCE_MANAGER_FULLTEXT_DIR` | Override fulltext directory |
 
-### Build
+## Data Format
 
-```bash
-npm run build
-```
+reference-manager uses [CSL-JSON](https://citeproc-js.readthedocs.io/en/latest/csl-json/markup.html) as its native format — the same format used by Pandoc, Zotero, and other academic tools.
 
-### Test
+### Pandoc Integration
 
 ```bash
-# Run all tests
-npm test
-
-# Watch mode
-npm run test:watch
-
-# Coverage
-npm run test:coverage
+# Export your library
+ref list --format json > references.json
+
+# Use with Pandoc
+pandoc manuscript.md \
+  --bibliography references.json \
+  --csl apa.csl \
+  -o manuscript.docx
 ```
 
-### Quality Checks
+### Custom Fields
+
+reference-manager extends CSL-JSON with a `custom` object for additional metadata:
+
+```json
+{
+  "id": "smith2024",
+  "type": "article-journal",
+  "title": "Example Paper",
+  "custom": {
+    "uuid": "550e8400-e29b-41d4-a716-446655440000",
+    "tags": ["important", "to-read"],
+    "fulltext_pdf": "smith2024.pdf",
+    "fulltext_md": "smith2024.md"
+  }
+}
+```
 
-```bash
-# Type checking
-npm run typecheck
+## Project Status
 
-# Linting
-npm run lint
+**Alpha** — This project is under active development. APIs and commands may change between versions.
 
-# Format
-npm run format
-```
+See [ROADMAP.md](./ROADMAP.md) for development progress and planned features.
 
-## Project Status
+## Development
 
-✅ **All phases completed** (Phase 1-5)
+### Build
 
-- 606 tests passing
-- Full TypeScript type coverage
-- Multi-platform support (Linux, macOS, Windows)
-- Ready for distribution
+```bash
+npm run build
+```
 
-## Architecture
+### Test
 
-The project is organized into modular components:
+```bash
+npm test                 # Run all tests
+npm run test:watch       # Watch mode
+npm run test:coverage    # Coverage report
+```
 
-- **Core**: CSL-JSON processing, Reference/Library management, Identifier generation
-- **Features**: Search, Duplicate detection, 3-way merge, File monitoring
-- **CLI**: Command-line interface with Commander.js
-- **Server**: HTTP server with Hono
-- **Utils**: Logging, File operations, Backup management
-- **Config**: TOML-based configuration
+### Quality Checks
 
-See `spec/_index.md` for detailed architecture documentation.
+```bash
+npm run typecheck        # TypeScript type checking
+npm run lint             # Linting
+npm run format           # Code formatting
+```
 
 ## License
 
 MIT
 
-## Repository
+## Links
 
-https://github.com/ncukondo/reference-manager
+- [Repository](https://github.com/ncukondo/reference-manager)
+- [npm Package](https://www.npmjs.com/package/@ncukondo/reference-manager)
+- [Issues](https://github.com/ncukondo/reference-manager/issues)
+- [Documentation](./spec/)