File Preprocessing Skill

{WORKSPACE} = timestamped run directory provided by the orchestrator (e.g., _workspace/run_20260404_153000).

Purpose

Convert non-text deliverable files (Excel, PowerPoint, Word, PDF, images) into LLM-readable Markdown format. This is Phase 0 of the defense pipeline — it runs BEFORE the deliverable analyst.

When to Use

• Input directory contains Excel, PowerPoint, Word, PDF, or image files
• Deliverables are not plain text
• Multiple files need to be combined into a single analyzable document

Input

Files placed in the designated input directory (default: input/).

Process

Step 1: Run Extraction Script

bash .claude/skills/01_file-preprocessing/scripts/run_extract.sh \
  input/ \
  {WORKSPACE}/00_preprocessed_input.md

The wrapper script (run_extract.sh) handles everything:

1. Checks if uv is installed
2. If not → auto-installs via curl (user-level, no sudo)
3. If auto-install fails → prints clear installation instructions with multiple install methods and stops
4. Runs uv run extract_files.py which auto-resolves Python dependencies (openpyxl, python-pptx, python-docx)

The script automatically:

• Scans all files in the input directory
• Extracts content from supported formats into Markdown tables and text
• Creates a file manifest ({WORKSPACE}/00_file_manifest.json)
• Flags PDF and image files as "LLM-Native" — these need the Read tool

Step 2: Handle LLM-Native Files

After the script runs, check {WORKSPACE}/00_file_manifest.json for llm_native_paths. For each:

• PDF files: Use the Read tool with pages parameter

  Read(file_path="/path/to/file.pdf", pages="1-10")

  Append the extracted content to {WORKSPACE}/00_preprocessed_input.md
• Image files: Use the Read tool (multimodal)

  Read(file_path="/path/to/image.png")

  Describe the image content and append to {WORKSPACE}/00_preprocessed_input.md

Step 3: Verify Output

Check that {WORKSPACE}/00_preprocessed_input.md contains meaningful content. If empty or minimal, report the issue.

Supported Formats

Output

• {WORKSPACE}/00_preprocessed_input.md — Combined Markdown with all extracted content
• {WORKSPACE}/00_file_manifest.json — Structured manifest of all input files

The deliverable-analyst agent reads 00_preprocessed_input.md as its input instead of raw files.