Paper Pilot

PaperPilot Workflow Instructions

When the user asks to "Run PaperPilot" or "analyze a paper", execute ALL of the following steps in order. Do not ask for clarification. Do not stop early. Complete all 7 steps.

Step 1: Scan the Input Folder

• List all files in: C:\Users\faizan\Desktop\PaperPilot\input\
• Identify the most recently added PDF file.
• If multiple PDFs exist, ask the user which one to process.
• If no PDFs exist, notify the user and stop.

Step 2: Extract Text from the PDF

• Use pdftotext or any available shell tool to extract text from the PDF.
• Save the raw text to: C:\Users\faizan\Desktop\PaperPilot\input\extracted.txt
• Identify the paper's title from the first few lines of the extracted text.
• Create a sanitized folder name from the title (e.g., "Attention_Is_All_You_Need").
• Call this variable PAPER_TITLE.

Step 3: Create the Output Workspace

• Create this directory: C:\Users\faizan\Desktop\PaperPilot\output\{PAPER_TITLE}\

Step 4: Generate Summary.md and Structured_Insights.md

• Read the full prompt from: C:\Users\faizan\Desktop\PaperPilot\prompts\analyze_paper.md
• Read the extracted text from Step 2.
• Using both as instructions, write TWO files to C:\Users\faizan\Desktop\PaperPilot\output\{PAPER_TITLE}\:
  • Summary.md — Problem, methodology, key results, one-line takeaway.
  • Structured_Insights.md — Dataset, model type, metrics table, reproducibility.

Step 5: Generate Research_Gap.md

• Read the full prompt from: C:\Users\faizan\Desktop\PaperPilot\prompts\research_gap.md
• Read the extracted text from Step 2.
• Using both as instructions, write Research_Gap.md to the output folder.
• It must contain: Methodological Gaps, Dataset/Evaluation Gaps, Reasoning Gaps, and Future Work proposals.

Step 6: Generate Related_Work.md (Browser Search)

• Open the browser.
• Search arXiv.org or Semantic Scholar for papers related to {PAPER_TITLE}.
• Identify exactly 3 highly relevant papers.
• For each paper, extract ONLY: Title, Year, and direct arXiv link.
• Write Related_Work.md to the output folder with this information.

Step 7: Finalize

• Create an empty file: C:\Users\faizan\Desktop\PaperPilot\output\{PAPER_TITLE}\Notes.txt
• Move the original PDF from the input folder to: C:\Users\faizan\Desktop\PaperPilot\output\{PAPER_TITLE}\original.pdf
• Delete C:\Users\faizan\Desktop\PaperPilot\input\extracted.txt
• Notify the user: "PaperPilot complete! Check output/{PAPER_TITLE}/ — all 5 files generated."

Rules

• Do NOT stop between steps to ask for permission.
• Do NOT treat this as a conversational request.
• Execute all 7 steps in sequence and call complete_task only after Step 7 is done.