[MODEL] Claude Code ignored prompt in plan mode

Preflight Checklist

• [x] I have searched existing issues for similar behavior reports
• [x] This report does NOT contain sensitive information (API keys, passwords, etc.)

Type of Behavior Issue

Claude ignored my instructions or configuration

What You Asked Claude to Do

/plan Plan removal of ophaned code and unused code paths. The latest experiments are defined in the notebooks @notebooks/experiments/ .

What Claude Actually Did

1. Claude enabled plan-mode
2. Claude loaded Skill 'init'
3. Claude explored the the codebase using 2 parallel Explore agents
4. Agents returned outputs; Claude then wrote a complete codebase structure for the CLAUDE.md documentation
5. Claude read README.md copilot-instructions.md and CLAUDE.md
6. Claude wrote a plan that would improve CLAUDE.md (prancy-mapping-reddy.md). The plan consists only of a rewrite for CLAUDE.md
7. Claude exits plan-mode
8. Claude exits plan-mode, but now accompanied with the plan

Expected Behavior

1. Claude enabled plan-mode
2. Claude read README.md
3. Claude loaded Skill 'init' [optionally]
4. Claude explored the the codebase [optionally using 2 parallel Explore agents]
5. Agents returned outputs
6. Claude wrote a plan that would list all orphaned code and unused code paths in the working directory, and describe a refactor procedure
7. Claude exits plan-mode accompanied with the plan

Files Affected

- README.md
- .github/copilot-instructions.md
- CLAUDE.md

Permission Mode

Accept Edits was OFF (manual approval required)

Can You Reproduce This?

Haven't tried to reproduce

Steps to Reproduce

_No response_

Claude Model

Sonnet

Relevant Conversation

Claude: I'll explore the codebase in parallel to understand the full structure before planning improvements to CLAUDE.md.
[explored directory]
Claude: Perfect! Now I have comprehensive understanding of the codebase. Let me create a detailed summary report:

## SNSolver_Package Comprehensive Codebase Analysis

Based on my thorough exploration, here is the complete codebase structure for your CLAUDE.md documentation:
[full explanation of codebase structure]

Claude: Let me read the existing CLAUDE.md, copilot instructions, and README to capture everything important before writing the improved plan.
[reads README, CLAUDE.md, and .github/copilot-instructions.md

Claude: Now I have everything I need. Let me write the plan file with the full improved CLAUDE.md content.
[proceeds to write plan and created a plan file at ~/.claude/plans/ , then exits plan mode]

Impact

Low - Minor inconvenience

Claude Code Version

2.1.128 (Claude Code)

Platform

Anthropic API

Additional Context

_No response_