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+# Scientific Paper Writer Configuration
+# Multi-stage system for writing publication-ready scientific papers
+# Features: Multi-stage creation process and special command system
+
+agents:
+  # Command processor for system navigation
+  command_processor:
+    type: llm
+    config:
+      provider: openai
+      model: gpt-4
+      temperature: 0.1
+      system_prompt: |
+        You are the command processor for a scientific paper writing system.
+        Process commands that start with "!" and route them appropriately.
+        
+        Available commands:
+        - !next [stage_name] - Proceed to next stage or specified stage
+        - !accept - Accept current content and move to next section/stage
+        - !help - List all available commands
+        - !stage - Show current stage and its purpose
+        - !stages - List all stages and mark current stage
+        - !context [N|all] - Show context (N hops back or all history)
+        
+        When processing commands, provide clear feedback about the action taken.
+        For non-command input, indicate it will be passed to the current stage.
+
+  # Introduction stage agent
+  intro_agent:
+    type: llm
+    config:
+      provider: openai
+      model: gpt-4
+      temperature: 0.7
+      system_prompt: |
+        Welcome to the Scientific Paper Writer! 
+        
+        This system will guide you through writing a publication-ready scientific paper
+        using a multi-stage process. The stages are:
+        
+        1. Introduction (current) - System overview and welcome
+        2. Discovery - Define paper parameters and requirements  
+        3. Brainstorming - Refine high-level ideas and components
+        4. Vetting - Research and compile high-quality sources
+        5. Structure - Define complete table of contents
+        6. Deep Research - Detailed research for each section
+        7. Core Content - Write main body sections
+        8. Framing Content - Write conclusion and abstract
+        9. Proofreading - Review for errors and consistency
+        10. Formatting - Convert to desired format and compile
+        
+        You can use commands like !next to proceed, !help for assistance,
+        or !stages to see your progress.
+
+  # Discovery stage agent  
+  discovery_agent:
+    type: llm
+    config:
+      provider: openai
+      model: gpt-4
+      temperature: 0.8
+      system_prompt: |
+        You are in the DISCOVERY stage of scientific paper writing.
+        
+        Your goal is to help define the parameters for the paper:
+        - Subject or general category
+        - Interesting insights or key points to cover
+        - Overall length of the paper
+        - Target audience
+        - Target publications for submission
+        - Paper format (IMPORTANT: currently only LaTeX is supported)
+        
+        When asked about format, only accept "latex" as an answer.
+        If user provides any other format, respond: "That format isn't supported yet. 
+        The only supported formats are: latex"
+        
+        Engage in conversation to gather all requirements that will constrain 
+        the writing process. Save the final requirements to context when complete.
+
+  # Brainstorming stage agent
+  brainstorming_agent:
+    type: llm
+    config:
+      provider: openai
+      model: gpt-4
+      temperature: 0.9
+      system_prompt: |
+        You are in the BRAINSTORMING stage of scientific paper writing.
+        
+        Work with the user to refine the high-level idea for the paper and 
+        identify fundamental components. Use the requirements from the Discovery
+        stage to guide the conversation.
+        
+        Focus on:
+        - Refining the core thesis or research question
+        - Identifying key arguments and supporting points
+        - Determining the logical flow of ideas
+        - Establishing the scope and boundaries
+        - Identifying potential challenges or counterarguments
+        
+        Save the refined concept and components to context when complete.
+
+  # Vetting stage agent
+  vetting_agent:
+    type: llm
+    config:
+      provider: openai
+      model: gpt-4
+      temperature: 0.3
+      system_prompt: |
+        You are in the VETTING stage of scientific paper writing.
+        
+        Your task is to research the topic at a high level and compile 
+        high-quality sources. For each source, provide:
+        - One page summary of the source
+        - Direct link/URL to retrieve the full text
+        - Complete bibliographic metadata (author, title, journal, etc.)
+        - Proper citation format
+        
+        Use web search capabilities to find authoritative, peer-reviewed sources.
+        Focus on recent publications and seminal works in the field.
+        Organize sources by relevance and quality.
+
+  # Structure stage agent
+  structure_agent:
+    type: llm
+    config:
+      provider: openai
+      model: gpt-4
+      temperature: 0.6
+      system_prompt: |
+        You are in the STRUCTURE stage of scientific paper writing.
+        
+        Create a complete table of contents with:
+        - All main sections and subsections
+        - 2-3 sentences describing the focus and purpose of each section
+        - Logical flow from introduction through conclusion
+        - Standard academic paper structure adapted to your topic
+        
+        Consider typical sections like:
+        - Abstract, Introduction, Literature Review
+        - Methodology, Results, Discussion
+        - Conclusion, References, Appendices (if needed)
+        
+        The descriptions will be replaced with full content in later stages.
+
+  # Deep research stage agent
+  deep_research_agent:
+    type: llm
+    config:
+      provider: openai
+      model: gpt-4
+      temperature: 0.4
+      system_prompt: |
+        You are in the DEEP RESEARCH stage of scientific paper writing.
+        
+        Research each section of the document in detail. For each section,
+        compile sources with:
+        - Complete bibliographic metadata and citations
+        - Summary of the source material
+        - Specific relevance to the section being written
+        - Key quotes or data points that support your arguments
+        
+        Use web search to find detailed, section-specific sources beyond
+        those found in the Vetting stage. Focus on depth and specificity.
+
+  # Core content writing agent
+  core_content_agent:
+    type: llm
+    config:
+      provider: openai
+      model: gpt-4
+      temperature: 0.7
+      system_prompt: |
+        You are in the CORE CONTENT stage of scientific paper writing.
+        
+        Write each section of the paper from top to bottom, one section at a time.
+        You have access to:
+        - Complete table of contents
+        - Paper summary from brainstorming
+        - All research sources and summaries
+        
+        Instructions:
+        - Write ONLY the section you're asked to write
+        - Do NOT write subsections under the current section yet
+        - Do NOT attempt to write other sections
+        - Use the research sources to support your arguments
+        - Follow academic writing standards
+        - Maintain consistent style and voice throughout
+        
+        Each subsection will be addressed separately to keep focus narrow.
+
+  # Framing content agent (conclusion and abstract)
+  framing_agent:
+    type: llm
+    config:
+      provider: openai
+      model: gpt-4
+      temperature: 0.6
+      system_prompt: |
+        You are in the FRAMING CONTENT stage of scientific paper writing.
+        
+        Write the Conclusion and Abstract sections based on the completed
+        main body of the paper. These sections should:
+        
+        Conclusion:
+        - Summarize key findings and arguments
+        - Address implications and significance
+        - Suggest future research directions
+        
+        Abstract:
+        - Concisely summarize the entire paper
+        - Include purpose, methods, key findings, conclusions
+        - Stay within word limits (typically 150-300 words)
+        
+        Both sections must accurately reflect the content in the main body.
+
+  # Proofreading agent
+  proofreading_agent:
+    type: llm
+    config:
+      provider: openai
+      model: gpt-4
+      temperature: 0.2
+      system_prompt: |
+        You are in the PROOFREADING stage of scientific paper writing.
+        
+        Review the complete paper for:
+        - Spelling and grammar errors
+        - Logical inconsistencies
+        - Factual errors or unsupported claims
+        - Unclear or awkward phrasing
+        - Active voice usage (prefer active over passive)
+        - Consistent terminology and style
+        - Proper citation format
+        - Flow and transitions between sections
+        
+        Make corrections while preserving the author's voice and intent.
+        Provide explanations for significant changes.
+
+  # Formatting agent using Gemini for large context
+  formatting_agent:
+    type: llm
+    config:
+      provider: google
+      model: gemini-pro-2.5
+      temperature: 0.1
+      system_prompt: |
+        You are in the FORMATTING stage of scientific paper writing.
+        
+        Convert the complete paper text into the specified format (currently LaTeX).
+        Your tasks:
+        - Convert all content to proper LaTeX format
+        - Include necessary packages and document structure
+        - Format citations, figures, tables properly
+        - Ensure compilation without errors
+        
+        After formatting, attempt to compile the LaTeX.
+        If compilation fails, analyze errors and fix them iteratively.
+        Only present the final result when it compiles successfully
+        and contains all original content.
+
+  # Content validator for formatting stage
+  content_validator:
+    type: llm
+    config:
+      provider: openai
+      model: gpt-4
+      temperature: 0.1
+      system_prompt: |
+        Validate that the formatted output contains all content from 
+        the original text. Compare the original text with the formatted
+        version and identify any missing content.
+        
+        If content is missing, provide specific details about what
+        is missing and where it should be located.
+
+# Routes for the multi-stage system
+routes:
+  # Main workflow coordinator
+  paper_writer:
+    type: graph
+    entry_point: start
+    
+    nodes:
+      # Command processing node
+      command_check:
+        type: conditional
+        condition:
+          type: content_starts_with
+          text: "!"
+          
+      # Command processor
+      process_command:
+        type: agent
+        agent: command_processor
+        
+      # Stage nodes
+      intro_stage:
+        type: agent
+        agent: intro_agent
+        
+      discovery_stage:
+        type: agent
+        agent: discovery_agent
+        
+      brainstorming_stage:
+        type: agent
+        agent: brainstorming_agent
+        
+      vetting_stage:
+        type: agent
+        agent: vetting_agent
+        
+      structure_stage:
+        type: agent
+        agent: structure_agent
+        
+      deep_research_stage:
+        type: agent
+        agent: deep_research_agent
+        
+      core_content_stage:
+        type: agent
+        agent: core_content_agent
+        
+      framing_stage:
+        type: agent
+        agent: framing_agent
+        
+      proofreading_stage:
+        type: agent
+        agent: proofreading_agent
+        
+      formatting_stage:
+        type: agent
+        agent: formatting_agent
+        
+      # Content validation
+      validate_content:
+        type: agent
+        agent: content_validator
+
+    edges:
+      # Initial routing
+      - source: start
+        target: command_check
+        
+      # Command processing path
+      - source: command_check
+        target: process_command
+        condition:
+          type: content_starts_with
+          text: "!"
+          
+      # Normal flow path (start with intro)
+      - source: command_check
+        target: intro_stage
+        condition:
+          type: always
+          
+      # Command processor can route to any stage based on commands
+      - source: process_command
+        target: intro_stage
+        condition:
+          type: content_contains
+          text: "intro"
+          
+      - source: process_command
+        target: discovery_stage
+        condition:
+          type: content_contains
+          text: "discovery"
+          
+      - source: process_command
+        target: brainstorming_stage
+        condition:
+          type: content_contains
+          text: "brainstorming"
+          
+      - source: process_command
+        target: vetting_stage
+        condition:
+          type: content_contains
+          text: "vetting"
+          
+      - source: process_command
+        target: structure_stage
+        condition:
+          type: content_contains
+          text: "structure"
+          
+      - source: process_command
+        target: deep_research_stage
+        condition:
+          type: content_contains
+          text: "deep_research"
+          
+      - source: process_command
+        target: core_content_stage
+        condition:
+          type: content_contains
+          text: "core_content"
+          
+      - source: process_command
+        target: framing_stage
+        condition:
+          type: content_contains
+          text: "framing"
+          
+      - source: process_command
+        target: proofreading_stage
+        condition:
+          type: content_contains
+          text: "proofreading"
+          
+      - source: process_command
+        target: formatting_stage
+        condition:
+          type: content_contains
+          text: "formatting"
+      
+      # Sequential stage flow (normal progression)
+      - source: intro_stage
+        target: discovery_stage
+        condition:
+          type: content_contains
+          text: "!next"
+          
+      - source: discovery_stage
+        target: brainstorming_stage
+        condition:
+          type: content_contains
+          text: "!next"
+          
+      - source: brainstorming_stage
+        target: vetting_stage
+        condition:
+          type: content_contains
+          text: "!next"
+          
+      - source: vetting_stage
+        target: structure_stage
+        condition:
+          type: content_contains
+          text: "!next"
+          
+      - source: structure_stage
+        target: deep_research_stage
+        condition:
+          type: content_contains
+          text: "!next"
+          
+      - source: deep_research_stage
+        target: core_content_stage
+        condition:
+          type: content_contains
+          text: "!next"
+          
+      - source: core_content_stage
+        target: framing_stage
+        condition:
+          type: content_contains
+          text: "!next"
+          
+      - source: framing_stage
+        target: proofreading_stage
+        condition:
+          type: content_contains
+          text: "!next"
+          
+      - source: proofreading_stage
+        target: formatting_stage
+        condition:
+          type: content_contains
+          text: "!next"
+          
+      # Formatting validation loop
+      - source: formatting_stage
+        target: validate_content
+        
+      - source: validate_content
+        target: formatting_stage
+        condition:
+          type: content_contains
+          text: "missing content"
+          
+      - source: validate_content
+        target: end
+        condition:
+          type: content_contains
+          text: "validation complete"
+
+  # Input stream handler
+  input_handler:
+    type: stream
+    stream_type: cold
+    operators:
+      - type: graph_execute
+        params:
+          graph: paper_writer
+    publications:
+      - __output__
+
+# Connect input to the workflow
+merges:
+  - sources: [__input__]
+    target: input_handler
+
+# Context management for the paper writing process
+context:
+  global:
+    app_name: "Scientific Paper Writer"
+    current_stage: "intro"
+    
+    # Stage definitions for reference
+    stages:
+      - name: "intro"
+        description: "Welcome and system introduction"
+        purpose: "Introduce the multi-stage paper writing system"
+        
+      - name: "discovery" 
+        description: "Requirements gathering"
+        purpose: "Define paper parameters, subject, audience, format, etc."
+        
+      - name: "brainstorming"
+        description: "Idea refinement"
+        purpose: "Refine high-level ideas and fundamental components"
+        
+      - name: "vetting"
+        description: "High-level research" 
+        purpose: "Research topic and compile high-quality sources with summaries"
+        
+      - name: "structure"
+        description: "Table of contents creation"
+        purpose: "Define complete paper structure with section descriptions"
+        
+      - name: "deep_research"
+        description: "Detailed section research"
+        purpose: "Research each section in detail with specific sources"
+        
+      - name: "core_content"
+        description: "Main content writing"
+        purpose: "Write paper sections one at a time from top to bottom"
+        
+      - name: "framing"
+        description: "Conclusion and abstract writing"
+        purpose: "Write conclusion and abstract based on completed content"
+        
+      - name: "proofreading"
+        description: "Review and correction"
+        purpose: "Proofread for errors, consistency, and style"
+        
+      - name: "formatting"
+        description: "Format conversion and compilation"
+        purpose: "Convert to LaTeX, compile, and validate completeness"
+    
+    # Paper state tracking
+    paper_state:
+      requirements: null
+      concept: null
+      sources: []
+      structure: null
+      sections: {}
+      current_section: null
+      format: null
+      final_text: null
+      latex_source: null
+      pdf_path: null
+      
+    # Command help text
+    commands:
+      "!next": "Proceed to next stage or specified stage: !next [stage_name]"
+      "!accept": "Accept current content and move to next section/stage"  
+      "!help": "List all available commands and their usage"
+      "!stage": "Show current stage name and detailed purpose"
+      "!stages": "List all stages with current stage marked"
+      "!context": "Show context: !context [N] (N hops back) or !context all"
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