@wentorai/research-plugins 1.0.0 → 1.2.0

package/skills/literature/metadata/zoplicate-dedup-guide/SKILL.md

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+---
+name: zoplicate-dedup-guide
+description: "Detect and manage duplicate items in Zotero libraries"
+metadata:
+  openclaw:
+    emoji: "🔃"
+    category: "literature"
+    subcategory: "metadata"
+    keywords: ["Zotero", "deduplication", "duplicate detection", "library cleanup", "metadata merge"]
+    source: "https://github.com/ChenglongMa/zoplicate"
+---
+
+# Zoplicate: Zotero Deduplication Guide
+
+## Overview
+
+Zoplicate is a Zotero plugin that detects and manages duplicate items in your library. It goes beyond Zotero's built-in duplicate detection by offering configurable matching criteria, batch merge operations, automatic deduplication on import, and smart metadata merging that keeps the best version of each field. Essential for researchers who import from multiple databases.
+
+## Installation
+
+```bash
+# Download .xpi from GitHub releases
+# Zotero 7: Tools → Add-ons → Install Add-on From File
+```
+
+## Features
+
+```markdown
+### Duplicate Detection
+- **DOI matching** — Most reliable, catches exact duplicates
+- **Title similarity** — Fuzzy matching for slight variations
+- **ISBN matching** — For books and proceedings
+- **Combined scoring** — Weighted match across multiple fields
+
+### Smart Merge
+- Keep the most complete metadata from each duplicate
+- Preserve all tags from both items
+- Merge notes and annotations
+- Consolidate attachments (keep all unique PDFs)
+- Maintain collection memberships from both
+
+### Automatic Mode
+- Detect duplicates on import
+- Configurable auto-merge threshold
+- Notification before auto-merge (optional)
+```
+
+## Configuration
+
+```json
+{
+  "detection": {
+    "criteria": {
+      "doi": {"enabled": true, "weight": 1.0},
+      "title": {"enabled": true, "weight": 0.8,
+                 "similarity_threshold": 0.85},
+      "isbn": {"enabled": true, "weight": 1.0},
+      "year_author": {"enabled": true, "weight": 0.6}
+    },
+    "overall_threshold": 0.7,
+    "ignore_case": true,
+    "normalize_unicode": true
+  },
+  "merge": {
+    "strategy": "keep_most_complete",
+    "preserve_tags": true,
+    "merge_notes": true,
+    "keep_all_attachments": true,
+    "prefer_fields_from": "newer"
+  },
+  "auto": {
+    "detect_on_import": true,
+    "auto_merge": false,
+    "notify_on_detect": true
+  }
+}
+```
+
+## Usage Workflow
+
+```markdown
+### Manual Deduplication
+1. Tools → Zoplicate → Find Duplicates
+2. Review duplicate groups (side-by-side comparison)
+3. Select master item for each group
+4. Click "Merge" — metadata combined, duplicates removed
+
+### Batch Operations
+1. Tools → Zoplicate → Find All Duplicates
+2. Review summary (X groups, Y total duplicates)
+3. "Auto-select best" — picks master by completeness
+4. "Merge All" — batch process all groups
+
+### Import Deduplication
+1. Import papers from database export (RIS, BibTeX)
+2. Zoplicate auto-checks against existing library
+3. Popup shows potential duplicates
+4. Choose: Skip / Merge / Import as new
+```
+
+## Matching Examples
+
+```markdown
+### DOI Match (100% confidence)
+Item A: "Attention Is All You Need" — DOI: 10.48550/arXiv.1706.03762
+Item B: "Attention is All You Need" — DOI: 10.48550/arXiv.1706.03762
+→ Exact duplicate (same DOI)
+
+### Title Fuzzy Match (85% similarity)
+Item A: "BERT: Pre-training of Deep Bidirectional Transformers..."
+Item B: "Bert: Pre-Training of Deep Bidirectional Transformers..."
+→ Likely duplicate (title similarity > threshold)
+
+### Different Versions (not duplicate)
+Item A: "Paper Title" (arXiv v1, 2023)
+Item B: "Paper Title" (Published version, 2024)
+→ Different DOIs, may want to keep both or merge
+```
+
+## Integration Tips
+
+```markdown
+### Multi-Database Import Workflow
+1. Search PubMed → Export RIS → Import to Zotero
+2. Search Scopus → Export RIS → Import to Zotero
+3. Search Web of Science → Export RIS → Import to Zotero
+4. Zoplicate detects cross-database duplicates
+5. Merge: keep best metadata from each source
+
+### With Other Plugins
+- **Zotero Connector** — Detect dups on browser import
+- **Better BibTeX** — Preserve citation keys on merge
+- **ZotMoov** — Reorganize attachments after merge
+```
+
+## Use Cases
+
+1. **Library cleanup**: Remove duplicates from large collections
+2. **Import dedup**: Prevent duplicates when importing from databases
+3. **Systematic reviews**: Deduplicate multi-database search results
+4. **Lab libraries**: Merge shared group library duplicates
+5. **Migration**: Clean up after importing from other reference managers
+
+## References
+
+- [Zoplicate GitHub](https://github.com/ChenglongMa/zoplicate)
+- [Zotero Duplicate Detection](https://www.zotero.org/support/duplicate_detection)

package/skills/literature/metadata/zotero-actions-tags-guide/SKILL.md

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+---
+name: zotero-actions-tags-guide
+description: "Zotero workflow automation with custom actions and tags"
+metadata:
+  openclaw:
+    emoji: "⚡"
+    category: "literature"
+    subcategory: "metadata"
+    keywords: ["Zotero", "automation", "tags", "workflow", "actions", "productivity"]
+    source: "https://github.com/windingwind/zotero-actions-tags"
+---
+
+# Zotero Actions & Tags Guide
+
+## Overview
+
+Zotero Actions & Tags is a powerful Zotero plugin that enables workflow automation through event-triggered actions. Define custom rules that execute when items are added, modified, opened, or tagged — such as auto-tagging by collection, running scripts on PDF open, auto-renaming attachments, or sending notifications. Transforms Zotero from a passive reference manager into an active research workflow engine.
+
+## Installation
+
+```bash
+# Download .xpi from GitHub releases
+# In Zotero 7: Tools → Add-ons → Install Add-on From File
+```
+
+## Core Concepts
+
+```markdown
+### Event → Condition → Action
+
+**Events** (triggers):
+- Item added to library
+- Item added to collection
+- Item modified
+- Tag added/removed
+- Attachment opened
+- Item selected
+
+**Conditions** (filters):
+- Item type (article, book, etc.)
+- Collection membership
+- Tag presence/absence
+- Field value match (regex)
+- Date range
+
+**Actions** (responses):
+- Add/remove tags
+- Set field values
+- Run JavaScript
+- Open URLs
+- Copy to clipboard
+- Show notifications
+```
+
+## Action Examples
+
+### Auto-Tag by Collection
+
+```json
+{
+  "name": "Auto-tag ML papers",
+  "event": "add_to_collection",
+  "condition": {
+    "collection": "Machine Learning"
+  },
+  "actions": [
+    {"type": "add_tag", "tag": "#ml"},
+    {"type": "add_tag", "tag": "#to-read"}
+  ]
+}
+```
+
+### Mark as Read on Open
+
+```json
+{
+  "name": "Track reading",
+  "event": "open_attachment",
+  "condition": {
+    "attachment_type": "application/pdf"
+  },
+  "actions": [
+    {"type": "remove_tag", "tag": "#to-read"},
+    {"type": "add_tag", "tag": "#reading"},
+    {"type": "set_field", "field": "extra",
+     "value": "LastOpened: ${date}"}
+  ]
+}
+```
+
+### Auto-Prioritize Highly Cited
+
+```json
+{
+  "name": "Flag high-impact",
+  "event": "item_modified",
+  "condition": {
+    "field": "extra",
+    "regex": "Citations:\\s*(\\d{3,})"
+  },
+  "actions": [
+    {"type": "add_tag", "tag": "#high-impact"},
+    {"type": "add_tag", "tag": "#priority"}
+  ]
+}
+```
+
+### Custom Script Action
+
+```javascript
+// Run custom JavaScript on trigger
+// Example: Auto-format author names
+{
+  "name": "Format authors",
+  "event": "item_added",
+  "action": {
+    "type": "script",
+    "code": `
+      const creators = item.getCreators();
+      // Log to Zotero debug console
+      Zotero.debug('New item by: ' +
+        creators.map(c => c.lastName).join(', '));
+    `
+  }
+}
+```
+
+## Workflow Recipes
+
+### Reading Pipeline
+
+```json
+[
+  {
+    "name": "New → To-Read",
+    "event": "item_added",
+    "actions": [{"type": "add_tag", "tag": "#to-read"}]
+  },
+  {
+    "name": "To-Read → Reading",
+    "event": "open_attachment",
+    "condition": {"has_tag": "#to-read"},
+    "actions": [
+      {"type": "remove_tag", "tag": "#to-read"},
+      {"type": "add_tag", "tag": "#reading"}
+    ]
+  },
+  {
+    "name": "Reading → Done",
+    "event": "tag_added",
+    "condition": {"tag": "#done"},
+    "actions": [
+      {"type": "remove_tag", "tag": "#reading"}
+    ]
+  }
+]
+```
+
+### Auto-Organization
+
+```json
+[
+  {
+    "name": "Tag by journal",
+    "event": "item_added",
+    "condition": {
+      "field": "publicationTitle",
+      "regex": "Nature|Science|Cell"
+    },
+    "actions": [
+      {"type": "add_tag", "tag": "#top-journal"}
+    ]
+  },
+  {
+    "name": "Flag recent papers",
+    "event": "item_added",
+    "condition": {
+      "field": "date",
+      "after": "2024-01-01"
+    },
+    "actions": [
+      {"type": "add_tag", "tag": "#recent"}
+    ]
+  }
+]
+```
+
+## Configuration
+
+```markdown
+### Settings (Edit → Preferences → Actions & Tags)
+
+- **Enable/disable** individual actions
+- **Action priority** — execution order when multiple match
+- **Logging** — debug action execution
+- **Import/Export** — share action sets with collaborators
+- **Keyboard shortcuts** — trigger actions manually
+```
+
+## Use Cases
+
+1. **Reading workflow**: Auto-track reading status via tags
+2. **Auto-organization**: Tag by collection, journal, or date
+3. **Priority flagging**: Highlight high-impact or recent papers
+4. **Team workflows**: Shared tag-based review pipelines
+5. **Custom scripts**: Extend Zotero with JavaScript actions
+
+## References
+
+- [Zotero Actions & Tags GitHub](https://github.com/windingwind/zotero-actions-tags)
+- [Zotero JavaScript API](https://www.zotero.org/support/dev/client_coding/javascript_api)
+- [Zotero Plugin Development](https://www.zotero.org/support/dev/client_coding/plugin_development)

package/skills/literature/metadata/zotmoov-guide/SKILL.md

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+---
+name: zotmoov-guide
+description: "Zotero plugin for automatic attachment file organization"
+metadata:
+  openclaw:
+    emoji: "📂"
+    category: "literature"
+    subcategory: "metadata"
+    keywords: ["Zotero", "file management", "attachment", "auto-move", "organization", "linked files"]
+    source: "https://github.com/wileyyugioh/zotmoov"
+---
+
+# ZotMoov Guide
+
+## Overview
+
+ZotMoov is a Zotero plugin that automatically moves and renames attachment files (PDFs, supplementary materials) to a designated directory with customizable naming patterns. It keeps your PDFs organized in a structured folder hierarchy outside Zotero's storage, using linked files instead of copies. Essential for researchers who want clean file organization alongside Zotero's metadata management.
+
+## Installation
+
+```bash
+# Download .xpi from GitHub releases
+# Zotero 7: Tools → Add-ons → Install Add-on From File
+```
+
+## Configuration
+
+```markdown
+### Settings (Edit → Preferences → ZotMoov)
+
+**Destination Directory:**
+~/Papers/  (your organized PDF library)
+
+**File Naming Pattern:**
+{%a}_{%y}_{%t}.pdf
+→ Vaswani_2017_Attention Is All You Need.pdf
+
+**Folder Structure:**
+{%y}/{%j}/
+→ 2017/NeurIPS/Vaswani_2017_Attention.pdf
+
+**Available Variables:**
+- {%a} — First author last name
+- {%y} — Publication year
+- {%t} — Title (truncated)
+- {%j} — Journal/venue
+- {%T} — Item type
+- {%c} — Collection name
+```
+
+## Naming Patterns
+
+```markdown
+### Common Patterns
+
+**Author_Year_Title:**
+{%a}_{%y}_{%t}
+→ Vaswani_2017_Attention Is All You Need
+
+**Year/Author-Title:**
+{%y}/{%a} - {%t}
+→ 2017/Vaswani - Attention Is All You Need
+
+**Collection/Author_Year:**
+{%c}/{%a}_{%y}_{%t}
+→ Transformers/Vaswani_2017_Attention Is All You Need
+
+**Journal/Year/Author:**
+{%j}/{%y}/{%a}_{%t}
+→ NeurIPS/2017/Vaswani_Attention Is All You Need
+```
+
+## Workflow
+
+```markdown
+### Automatic Mode
+1. Add paper to Zotero (browser connector, DOI import)
+2. ZotMoov detects new attachment
+3. Moves PDF to destination with naming pattern
+4. Converts to linked file in Zotero
+5. Original storage location freed
+
+### Manual Mode
+1. Select items in Zotero
+2. Right-click → ZotMoov → Move Attachments
+3. Bulk processing for existing library
+
+### Reverse (Undo)
+1. Right-click → ZotMoov → Move to Zotero Storage
+2. Converts back to stored file
+```
+
+## Integration with Other Tools
+
+```markdown
+### Synced PDF Library
+ZotMoov + cloud sync = PDFs accessible everywhere:
+- Move to Dropbox/OneDrive/Google Drive folder
+- Zotero metadata synced via Zotero Sync
+- PDFs synced via cloud provider
+- Access on any device with cloud sync
+
+### With Other Plugins
+- **Better BibTeX**: Use citekey in file name: {%b}.pdf
+- **Zotero Style**: Visual indicators for linked vs stored
+- **Zoplicate**: Handles duplicates before moving
+```
+
+## Use Cases
+
+1. **File organization**: Structured PDF library outside Zotero
+2. **Cloud sync**: PDFs in Dropbox/OneDrive for multi-device
+3. **Backup strategy**: Separate PDF backup from Zotero data
+4. **Naming convention**: Consistent file naming across library
+5. **Storage management**: Free Zotero storage space
+
+## References
+
+- [ZotMoov GitHub](https://github.com/wileyyugioh/zotmoov)
+- [Zotero Linked Files](https://www.zotero.org/support/attaching_files)

package/skills/literature/metadata/zutilo-guide/SKILL.md

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+---
+name: zutilo-guide
+description: "Zotero utility plugin for keyboard shortcuts and batch editing"
+metadata:
+  openclaw:
+    emoji: "⌨️"
+    category: "literature"
+    subcategory: "metadata"
+    keywords: ["Zotero", "shortcuts", "batch editing", "utility", "productivity", "copy paste"]
+    source: "https://github.com/wshanks/Zutilo"
+---
+
+# Zutilo Guide
+
+## Overview
+
+Zutilo is a Zotero utility plugin that adds keyboard shortcuts, batch editing capabilities, and clipboard operations for efficient library management. It enables power-user workflows — copying/pasting tags between items, batch-editing fields, assigning keyboard shortcuts to any Zotero action, and quick item manipulation. Essential for researchers managing large collections who need speed and efficiency.
+
+## Installation
+
+```bash
+# Download .xpi from GitHub releases
+# Zotero 7: Tools → Add-ons → Install Add-on From File
+```
+
+## Key Features
+
+### Clipboard Operations
+
+```markdown
+### Tag Management
+- **Copy tags** from selected item(s)
+- **Paste tags** to selected item(s)
+- **Remove tags** from selected item(s) by clipboard
+- Supports multiple items simultaneously
+
+### Field Operations
+- Copy creator (author) information
+- Paste creators to other items
+- Copy item fields to clipboard
+- Batch copy/paste between items
+
+### Related Items
+- Copy related item links
+- Paste related items in bulk
+- Quick-link items as related
+```
+
+### Keyboard Shortcuts
+
+```markdown
+### Configurable Shortcuts
+Zutilo lets you assign keyboard shortcuts to:
+- Copy/paste tags
+- Copy/paste related items
+- Edit item info
+- Open attachment
+- Show/hide panes
+- Merge duplicates
+- Any Zotero menu action
+
+### Common Shortcuts Setup
+Ctrl+Shift+C → Copy tags
+Ctrl+Shift+V → Paste tags
+Ctrl+Shift+R → Copy related items
+Alt+E → Edit item
+Alt+O → Open first attachment
+```
+
+### Batch Operations
+
+```markdown
+### Batch Tag Editing
+1. Select multiple items (Ctrl+Click or Shift+Click)
+2. Zutilo → Paste Tags (applies to all selected)
+3. Or: Zutilo → Remove Tags (removes from all selected)
+
+### Batch Field Editing
+- Modify item type for multiple items
+- Batch-update a field value
+- Copy field from one item, paste to many
+
+### Item Manipulation
+- Merge items (combine metadata)
+- Relate items in batch
+- Move items between collections
+```
+
+## Configuration
+
+```markdown
+### Preferences (Edit → Preferences → Zutilo)
+
+**Shortcut Configuration:**
+- Each Zutilo function can have a keyboard shortcut
+- Shortcuts: single key, Ctrl+key, or Ctrl+Shift+key
+- Avoid conflicts with existing Zotero shortcuts
+
+**Context Menu:**
+- Show/hide Zutilo items in right-click menu
+- Configure which operations appear
+- Group by category (tags, fields, related)
+
+**Behavior:**
+- Tag paste mode: append (default) or replace
+- Clipboard format: plain text or JSON
+- Confirm before batch operations: on/off
+```
+
+## Workflow Examples
+
+```markdown
+### Organize by Reading Status
+1. Create tag set: #to-read, #reading, #done
+2. Select papers to read → Ctrl+Shift+V (paste #to-read)
+3. As you finish → Copy #done tag → Select item → Paste
+
+### Bulk Relate Papers
+1. Select all papers on a topic
+2. Zutilo → Relate Selected Items
+3. All items now linked as related in Zotero
+
+### Migrate Tags
+1. Select items with old tag
+2. Copy tags → modify in text editor → Paste new tags
+3. Remove old tags in batch
+```
+
+## Use Cases
+
+1. **Power-user efficiency**: Keyboard-driven library management
+2. **Batch operations**: Tag and edit multiple items at once
+3. **Organization**: Quick tag assignment and removal
+4. **Workflow speed**: Reduce clicks in repetitive tasks
+5. **Collection management**: Efficient item relationships
+
+## References
+
+- [Zutilo GitHub](https://github.com/wshanks/Zutilo)
+- [Zotero Keyboard Shortcuts](https://www.zotero.org/support/kb)