[BUG] Pre-approved bash commands from completed tasks persist across sessions, causing re-execution of finished work

Environment

• Platform (select one):
• [ ] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [X] Other: <!-- specify --> Claude CLI
• Claude CLI version: <!-- output of claude --version --> 1.0.67 (Claude Code)
• Operating System: <!-- e.g. macOS 14.3, Windows 11, Ubuntu 22.04 --> macOS 15.5
• Terminal: <!-- e.g. iTerm2, Terminal App --> Terminal App

Description

Claude Code is caching and injecting pre-approved bash commands from previous sessions into new sessions, causing Claude Code to attempt re-executing already completed tasks. These commands appear in the system prompt under "tools without requiring user approval" and persist even after:

• Exiting Claude Code completely
• Starting a fresh session
• Tasks being clearly marked as COMPLETE in project documentation

Steps to Reproduce

1. Have CLAUDE.md load CLAUDE_RESUME.md with current completed and uncompleted tasks.
2. Have Claude execute bash commands for extracting document sections (e.g., using sed to split a markdown file)
3. Complete the task and mark it as done in CLAUDE_RESUME.md
4. Exit Claude Code (/exit)
5. Start a new session with claude .
6. Claude immediately attempts to re-execute the same extraction commands

Expected Behavior

• Pre-approved commands should be cleared between sessions
• Claude should follow the project's defined startup sequence (checking CLAUDE_RESUME.md

first)

• Completed tasks should not be re-attempted

Actual Behavior

• Old bash commands persist in the "tools without requiring user approval" section
• These appear to be interpreted as pending tasks rather than just available tools
• Claude attempts to re-execute completed work, ignoring CLAUDE_RESUME.md that clearly states the task is "✅ COMPLETED - DO NOT REPEAT"

Evidence

Session JSONL shows:

• User input: "."
• Claude's response: "I'll help you extract the individual sections from the v0.92 document..."
• Despite CLAUDE_RESUME.md stating this task is complete

Environment

• Claude Code version: 1.0.67
• Platform: macOS 15.5 Darwin 24.5.0
• Project type: Non-git project with markdown documentation

Workaround

Start sessions with explicit directive instead of just ".":
claude . "Check CLAUDE_RESUME.md for current status"

Impact

• Causes confusion and wasted effort
• Breaks carefully designed context management systems
• Forces users to interrupt Claude to prevent duplicate work
• Undermines project documentation that tracks completed tasks

Suggested Fix

• Clear pre-approved commands cache when session ends
• Add an option to clear commands cache
• Don't persist task-specific commands between sessions
• Or distinguish between "available tools" and "tasks to execute"