Development Session Handoff - July 10, 2025

what i was working on

The user ran /planning Website to understand what needed to be done, then /structural-editing de-darwinization.md to restructure the de-darwinization wiki article. The real problem was that Gemini's structural analysis gives unreliable line numbers, making the editing workflow broken.

I ended up discovering a critical issue: Gemini truncates content when lines exceed ~1200 characters. This wasn't a simple line-based editing problem - it was a fundamental limitation that causes content loss.

what got done

• Fixed the structural editing workflow: Updated /mnt/d/Coding/.claude/commands/structural-editing.md to use content-based operations instead of line numbers
• Updated root CLAUDE.md: Added gemini CLI syntax documentation and timeout requirements (all gemini commands need 10-minute timeout)
• Restructured de-darwinization article: Created v2 with better problem → framework → evidence → mechanisms flow by moving the challenges section to the introduction
• Solved the Gemini truncation problem: Processed v4 to split all lines over 1200 characters into readable paragraphs
• Updated CLAUDE.md with troubleshooting: Added section on why Gemini returns empty files when asked to "return the complete document"

The de-darwinization article now flows much better: challenges introduced upfront, Principal-Agent Problem provides conceptual framework, evidence supports the theory, then mechanisms explain the "how."

what's not working

Nothing broken right now. The content-based editing workflow works, and v4 has proper paragraph breaks without content loss.

current state

• System: WSL2 Ubuntu, gemini CLI working from /mnt/d/Coding directory
• Last working commands:

  # Gemini analysis (works with 10-minute timeout)
  gemini -p "@Website/docs/wiki/concepts/de-darwinization-v2.md Add paragraph breaks..." > output.md
  
  # Manual line splitting (what actually worked)
  awk 'length($0) > 1200 {print NR ":" length($0)}' file.md | sort -t: -k2 -nr
  sed -n '37p' file.md | sed 's/\. /.\n/g' > temp.txt
  

• Files I changed:
• /mnt/d/Coding/.claude/commands/structural-editing.md - converted to content-based operations
• /mnt/d/Coding/CLAUDE.md - added gemini syntax docs and timeout requirements
• Website/docs/wiki/concepts/de-darwinization-v4.md - final version with proper paragraph breaks

next steps

1. Use v4 as the canonical version - it has all the content from v2 but with readable paragraph breaks
2. Apply this workflow to other academic documents - any file with mega-lines will hit the same Gemini truncation issue
3. Document the line-length discovery - this is a real limitation that affects any Gemini text processing

for context

• The core discovery: Gemini truncates content at ~1200 characters per line, not just for output but during processing
• Check gemini-output/structural-analysis-20250709-210148.md for the original flawed analysis that started this investigation
• The Website project needed structural editing but the tooling was broken - now it's fixed
• All gemini commands need {"timeout": 600000} because it takes time to read large files, even for simple questions

why this matters

This session uncovered a fundamental limitation in using Gemini for document processing. The line-length issue will affect any technical document with dense paragraphs. The solution (manual line-breaking) works but needs to be applied preventively.

The content-based editing workflow is now solid and can handle complex academic documents without data loss. Future editors can use v4 as a reference for proper paragraph structure while preserving scholarly rigor.