[BUG] Clarifcation about correct settings.json format needed

[MikeeI]

Environment

• Platform (select one):
  • Anthropic API
  • AWS Bedrock
  • Google Vertex AI
  • Other:
• Claude CLI version: 1.0.6 (Claude Code)
• Operating System: Ubuntu 22.04 (Linux 5.15.0-139-generic x86_64)
• Terminal: xterm-256color (VSCode)

Bug Description

Claude Code repeatedly asks to run list and read commands for directories and files it has already accessed during long coding sessions, even though it clearly has this information from earlier in the same session.

Steps to Reproduce

1. Start a coding session in a project directory using Claude Code
2. Work for an extended period (typically after 30+ minutes of active coding)
3. Notice Claude Code asking to run list commands for directories it has already listed
4. Also occurs with read commands for files it has already accessed

Expected Behavior

Claude Code should remember directory contents and file contents from earlier in the same session without repeatedly requesting the same information.

Actual Behavior

Claude Code asks to re-run list and read commands for directories and files it has already processed, interrupting the coding workflow and creating redundant operations.

Additional Context

This appears to be a context/memory management issue where Claude Code loses track of what information it has already gathered during longer coding sessions. The behavior interrupts productivity as it repeatedly requests information it already possesses.

Current settings.json configuration:

{
	"permissions": {
		"allow": [
			"*",
			"Agent(*)",
			"Agent",
			"Bash(*)",
			"Bash",
			"Edit(*)",
			"Edit",
			"Find(*)",
			"Glob(*)",
			"Glob",
			"Grep(*)",
			"Grep",
			"LS(*)",
			"LS",
			"List(*)",
			"List",
			"NotebookEdit(*)",
			"NotebookEdit",
			"NotebookRead(*)",
			"NotebookRead",
			"Read(*)",
			"Read",
			"Search",
			"Search(*)",
			"WebFetch(*)",
			"WebFetch",
			"WebFetch(domain:docs.anthropic.com)",
			"WebFetch(domain:github.com)",
			"WebFetch(domain:gitlab.com)",
			"Write(*)",
			"Write"
		],
		"deny": []
	}
}

What is the right settings.json format to not have this problem anymore?

[bcherny]

Hi! Could you share the specific commands that are causing Claude to ask for permission?

[MikeeI]

This should be a simple read, but i m still asked

Welcome to Claude Code!

/help for help, /status for your current setup

cwd: /root/projects/project-github-search

Tip: Send messages to Claude while it works to steer Claude in real-time

> Try "how do I log an error?"
? for shortcuts

> /user:pr-cognitive-load-plus is running... 

✢ Schlepping... (8s · ⚒ 586 tokens · esc to interrupt)
✽ Schlepping... (9s · 587 tokens · esc to interrupt)
✻ Thinking...

The user wants me to analyze this repository and propose 5 high-impact, well-scoped PRs that address significant cognitive load issues through architectural and structural improvements. Let me analyze the codebase to understand its structure and identify areas where cognitive complexity can be reduced.

First, let me explore the codebase to understand its architecture:

From the directory structure, I can see this is a GitHub search tool that downloads Claude Code ecosystem files. The key components include:

1. scripts/ - Main download scripts
2. scripts/lib/ - Modular library system 
3. test/ - Testing framework
4. config/ - Configuration management
5. data/ - Output data storage

Let me examine the codebase structure more deeply to identify architectural complexity and cognitive load issues.

● I'll analyze this repository to identify architectural cognitive load issues and propose 5 high-impact PRs. Let me first explore the codebase structure and patterns.

● Task(Analyze codebase architecture)...
  ⎿  List(.)...

Read file

List(.)

Do you want to proceed?
❯ 1. Yes
  2. No, and tell Claude what to do differently (esc)