Add Skill: literature-review-with-traceable-ai-evidence

Extracted from: https://github.com/0verL1nk/PaperSage.git
Score: 1.0

skills/langgraph-csv-workflow/SKILL.md

@@ -1,89 +0,0 @@
----
-name: langgraph-csv-workflow
-version: 1.0.0
-description: Transform simple CSV files into powerful AI agent workflows using LangGraph
-  orchestration
-inputs:
-- 'CSV workflow files with columns: graph_name, node_name, agent_type, next_node,
-  on_failure, prompt, input_fields, output_field'
-- LLM provider configuration (OpenAI, Anthropic, Google) in agentmap_config.yaml
-- Storage configuration for CSV/JSON/Vector DBs in agentmap_config_storage.yaml
-steps:
-- Define workflow in CSV format specifying graph nodes, agent types, and data flow
-  between them
-- Configure LLM providers and storage backends in the agentmap configuration files
-- Execute the workflow using the agentmap CLI or Python API
-outputs:
-- Executed workflow with agent decisions and state transitions
-- Traced execution path through the graph nodes
-- Logged agent interactions and output fields populated
-tags: []
-metadata:
-  source_repo: https://github.com/jwwelbor/AgentMap.git
-  extracted_at: ''
-  confidence: 0.95
----
-
-# langgraph-csv-workflow
-
-Transform simple CSV files into powerful AI agent workflows using LangGraph orchestration
-
-## Setup
-
-**Dependencies:**
-
-```text
-pip install langgraph>=1.0.0 langchain-core>=0.3.0 pyyaml fastapi uvicorn
-```
-
-**Setup steps:**
-
-1. Install agentmap: pip install agentmap[all]
-1. Initialize configuration: agentmap init-config
-1. Configure LLM providers in agentmap_config.yaml
-1. Run workflow: agentmap run workflow.csv
-
-## Key Files
-
-- `agentmap_config.yaml - Main configuration for LLM providers and paths`
-- `agentmap_config_storage.yaml - Storage configuration for CSV/JSON/Vector DBs`
-- `hello_world.csv - Sample workflow definition`
-
-## Steps
-
-1. Define workflow in CSV format specifying graph nodes, agent types, and data flow between them
-2. Configure LLM providers and storage backends in the agentmap configuration files
-3. Execute the workflow using the agentmap CLI or Python API
-
-## Implementation Details
-
-```python
-CSV format: graph_name,node_name,agent_type,next_node,on_failure,prompt,input_fields,output_field
-```
-
-```python
-CLI command: agentmap run hello_world.csv --pretty
-```
-
-## Inputs
-
-- CSV workflow files with columns: graph_name, node_name, agent_type, next_node, on_failure, prompt, input_fields, output_field
-- LLM provider configuration (OpenAI, Anthropic, Google) in agentmap_config.yaml
-- Storage configuration for CSV/JSON/Vector DBs in agentmap_config_storage.yaml
-
-## Outputs
-
-- Executed workflow with agent decisions and state transitions
-- Traced execution path through the graph nodes
-- Logged agent interactions and output fields populated
-
-## Failure Modes
-
-- Invalid CSV format causing parse errors during workflow loading
-- Missing or misconfigured LLM provider credentials leading to runtime failures
-- Incorrect agent configuration (e.g., missing input_fields) causing processing errors
-
-## Source
-
-Extracted from: [https://github.com/jwwelbor/AgentMap.git](https://github.com/jwwelbor/AgentMap.git)
-Confidence: 0.95

skills/langgraph-csv-workflow/commands.md

@@ -1,6 +0,0 @@
-# Commands: langgraph-csv-workflow
-
-## Available Commands
-
-- `/skill langgraph-csv-workflow` — Load this skill
-- `/run langgraph-csv-workflow` — Execute workflow

skills/langgraph-csv-workflow/examples.md

@@ -1,10 +0,0 @@
-# Examples: langgraph-csv-workflow
-
-## Usage Example
-
-```python
-# How to use this skill
-# Inputs: CSV workflow files with columns: graph_name, node_name, agent_type, next_node, on_failure, prompt, input_fields, output_field, LLM provider configuration (OpenAI, Anthropic, Google) in agentmap_config.yaml, Storage configuration for CSV/JSON/Vector DBs in agentmap_config_storage.yaml
-# Process: Define workflow in CSV format specifying graph nodes, agent types, and data flow between them → Configure LLM providers and storage backends in the agentmap configuration files → Execute the workflow using the agentmap CLI or Python API
-# Outputs: Executed workflow with agent decisions and state transitions, Traced execution path through the graph nodes, Logged agent interactions and output fields populated
-```

skills/langgraph-csv-workflow/metadata.json

@@ -1,29 +0,0 @@
-{
-  "name": "langgraph-csv-workflow",
-  "version": "1.0.0",
-  "goal": "Transform simple CSV files into powerful AI agent workflows using LangGraph orchestration",
-  "inputs": [
-    "CSV workflow files with columns: graph_name, node_name, agent_type, next_node, on_failure, prompt, input_fields, output_field",
-    "LLM provider configuration (OpenAI, Anthropic, Google) in agentmap_config.yaml",
-    "Storage configuration for CSV/JSON/Vector DBs in agentmap_config_storage.yaml"
-  ],
-  "steps": [
-    "Define workflow in CSV format specifying graph nodes, agent types, and data flow between them",
-    "Configure LLM providers and storage backends in the agentmap configuration files",
-    "Execute the workflow using the agentmap CLI or Python API"
-  ],
-  "outputs": [
-    "Executed workflow with agent decisions and state transitions",
-    "Traced execution path through the graph nodes",
-    "Logged agent interactions and output fields populated"
-  ],
-  "failure_modes": [
-    "Invalid CSV format causing parse errors during workflow loading",
-    "Missing or misconfigured LLM provider credentials leading to runtime failures",
-    "Incorrect agent configuration (e.g., missing input_fields) causing processing errors"
-  ],
-  "confidence": 0.95,
-  "explanation": "AgentMap provides a declarative pattern where workflows are defined in CSV files with specific columns describing graph nodes, agent types, and data flow. This pattern can be adapted to create multi-agent systems with LangGraph, supporting various LLM providers and storage backends. The workflow is reusable across different use cases by simply modifying the CSV definition.",
-  "source_repo": "https://github.com/jwwelbor/AgentMap.git",
-  "score": 1.0
-}

skills/literature-review-with-traceable-ai-evidence/SKILL.md

@@ -0,0 +1,77 @@
+---
+name: literature-review-with-traceable-ai-evidence
+version: 1.0.0
+description: Enable researchers to ingest documents, asynchronously index them, and
+  interact with multi-agent AI to answer questions with verifiable citations to original
+  text.
+inputs:
+- Documents in PDF, Office, image, or text formats
+- Research questions or topics of interest
+- 'Optional: user model configuration via .env or settings'
+steps:
+- Upload documents to a project (via desktop app or web UI)
+- System asynchronously converts Office docs to PDF if needed, runs OCR to extract
+  text with coordinates, chunks and embeds into vector store
+- User starts a main research session or creates exploration branches without waiting
+  for indexing to finish
+- Leader agent receives query and delegates subtasks to researcher, reviewer, writer
+  subagents
+- Subagents perform hybrid retrieval and rerank to find relevant chunks with source
+  coordinates
+- Agents synthesize answers and return evidence with clickable citations that highlight
+  original pages
+- User verifies conclusions by navigating to cited source locations and can save notes
+  to research memory or mind map
+outputs:
+- AI-generated answers with traceable evidence (coordinates, page highlights)
+- Research session history with branches
+- Indexed document library for future queries
+- Mind maps or structured notes
+- Persistent run events for resuming sessions
+tags: []
+metadata:
+  source_repo: https://github.com/0verL1nk/PaperSage.git
+  extracted_at: ''
+  confidence: 0.85
+---
+
+# literature-review-with-traceable-ai-evidence
+
+Enable researchers to ingest documents, asynchronously index them, and interact with multi-agent AI to answer questions with verifiable citations to original text.
+
+## Steps
+
+1. Upload documents to a project (via desktop app or web UI)
+2. System asynchronously converts Office docs to PDF if needed, runs OCR to extract text with coordinates, chunks and embeds into vector store
+3. User starts a main research session or creates exploration branches without waiting for indexing to finish
+4. Leader agent receives query and delegates subtasks to researcher, reviewer, writer subagents
+5. Subagents perform hybrid retrieval and rerank to find relevant chunks with source coordinates
+6. Agents synthesize answers and return evidence with clickable citations that highlight original pages
+7. User verifies conclusions by navigating to cited source locations and can save notes to research memory or mind map
+
+## Inputs
+
+- Documents in PDF, Office, image, or text formats
+- Research questions or topics of interest
+- Optional: user model configuration via .env or settings
+
+## Outputs
+
+- AI-generated answers with traceable evidence (coordinates, page highlights)
+- Research session history with branches
+- Indexed document library for future queries
+- Mind maps or structured notes
+- Persistent run events for resuming sessions
+
+## Failure Modes
+
+- Missing local Office/LibreOffice converter causes document conversion failure
+- First-time model download may be slow or require network
+- OCR may have low confidence on poor quality scans
+- Retrieval might miss context if chunking splits semantics
+- Multi-agent coordination could produce conflicting intermediate results
+
+## Source
+
+Extracted from: [https://github.com/0verL1nk/PaperSage.git](https://github.com/0verL1nk/PaperSage.git)
+Confidence: 0.85

skills/literature-review-with-traceable-ai-evidence/commands.md

@@ -0,0 +1,6 @@
+# Commands: literature-review-with-traceable-ai-evidence
+
+## Available Commands
+
+- `/skill literature-review-with-traceable-ai-evidence` — Load this skill
+- `/run literature-review-with-traceable-ai-evidence` — Execute workflow

skills/literature-review-with-traceable-ai-evidence/examples.md

@@ -0,0 +1,10 @@
+# Examples: literature-review-with-traceable-ai-evidence
+
+## Usage Example
+
+```python
+# How to use this skill
+# Inputs: Documents in PDF, Office, image, or text formats, Research questions or topics of interest, Optional: user model configuration via .env or settings
+# Process: Upload documents to a project (via desktop app or web UI) → System asynchronously converts Office docs to PDF if needed, runs OCR to extract text with coordinates, chunks and embeds into vector store → User starts a main research session or creates exploration branches without waiting for indexing to finish
+# Outputs: AI-generated answers with traceable evidence (coordinates, page highlights), Research session history with branches, Indexed document library for future queries, Mind maps or structured notes, Persistent run events for resuming sessions
+```

skills/literature-review-with-traceable-ai-evidence/metadata.json

@@ -0,0 +1,37 @@
+{
+  "name": "literature-review-with-traceable-ai-evidence",
+  "version": "1.0.0",
+  "goal": "Enable researchers to ingest documents, asynchronously index them, and interact with multi-agent AI to answer questions with verifiable citations to original text.",
+  "inputs": [
+    "Documents in PDF, Office, image, or text formats",
+    "Research questions or topics of interest",
+    "Optional: user model configuration via .env or settings"
+  ],
+  "steps": [
+    "Upload documents to a project (via desktop app or web UI)",
+    "System asynchronously converts Office docs to PDF if needed, runs OCR to extract text with coordinates, chunks and embeds into vector store",
+    "User starts a main research session or creates exploration branches without waiting for indexing to finish",
+    "Leader agent receives query and delegates subtasks to researcher, reviewer, writer subagents",
+    "Subagents perform hybrid retrieval and rerank to find relevant chunks with source coordinates",
+    "Agents synthesize answers and return evidence with clickable citations that highlight original pages",
+    "User verifies conclusions by navigating to cited source locations and can save notes to research memory or mind map"
+  ],
+  "outputs": [
+    "AI-generated answers with traceable evidence (coordinates, page highlights)",
+    "Research session history with branches",
+    "Indexed document library for future queries",
+    "Mind maps or structured notes",
+    "Persistent run events for resuming sessions"
+  ],
+  "failure_modes": [
+    "Missing local Office/LibreOffice converter causes document conversion failure",
+    "First-time model download may be slow or require network",
+    "OCR may have low confidence on poor quality scans",
+    "Retrieval might miss context if chunking splits semantics",
+    "Multi-agent coordination could produce conflicting intermediate results"
+  ],
+  "confidence": 0.85,
+  "explanation": "The README describes PaperSage's core workflow: asynchronous document ingestion with OCR/indexing, followed by multi-agent question answering with cited evidence. This process is not tied to the specific codebase and can be reused as a general literature review methodology for any document-centric research using RAG and agent collaboration.",
+  "source_repo": "https://github.com/0verL1nk/PaperSage.git",
+  "score": 1.0
+}

skills/literature-review-with-traceable-ai-evidence/tests.md

@@ -1,4 +1,4 @@
-# Tests: langgraph-csv-workflow
+# Tests: literature-review-with-traceable-ai-evidence
 
 ## Test Checklist