Claude Code asks for permission before modifying files or running shell commands. Sometimes it gets stuck in a loop of permission denials, or you accidentally denied something you need. Here’s how to fix it.

The permission system

Claude Code has three permission levels:

Action	Default	Can auto-approve
Read files	✅ Auto-approved	Always
Write files	❓ Asks first	Yes, configurable
Shell commands	❓ Asks first	Yes, configurable
Delete files	❓ Asks first	Yes, configurable
Network access	❓ Asks first	Yes, configurable

When Claude asks “Allow this action?” and you press n, it remembers that denial for the session.

Fix 1: Reset session permissions

If you accidentally denied a permission:

# Start a new session (clears all permission decisions)
/clear

# Or rewind to before the denial
# Double-tap Esc

There’s no way to un-deny a specific permission within a session. Starting fresh or rewinding is the cleanest fix.

Fix 2: Configure auto-approve in settings

For actions you always want to allow:

// .claude/settings.json in your project root
{
  "permissions": {
    "allow": [
      "read_file",
      "list_directory",
      "search_files",
      "write_file",
      "shell_command"
    ],
    "deny": [
      "delete_file"
    ]
  }
}

This auto-approves file writes and shell commands while still blocking deletions. Adjust based on your trust level.

Warning: Auto-approving shell commands means Claude can run anything without asking. Only do this on projects where you trust the codebase and have git to revert changes.

Fix 3: Directory access issues

Claude Code can only access files in your current working directory and subdirectories:

# This works
cd /Users/you/project
claude "Read src/app.ts"

# This fails — outside project directory
claude "Read /etc/hosts"
claude "Read ../other-project/file.ts"

If you need Claude to access files outside the project:

# Option 1: Start Claude from a parent directory
cd /Users/you
claude "Compare project-a/src/auth.ts with project-b/src/auth.ts"

# Option 2: Copy the file into your project
cp ../other-project/reference.ts ./tmp/
claude "Read tmp/reference.ts for reference"

Fix 4: Shell command blocked by OS

On macOS, the system might block Claude’s shell commands:

# If you see "Operation not permitted"
# Grant Terminal full disk access:
# System Settings → Privacy & Security → Full Disk Access → Add Terminal

On Linux, SELinux or AppArmor might interfere:

# Check SELinux
getenforce
# If "Enforcing", temporarily set to permissive for testing
sudo setenforce 0

Fix 5: npm/pip permission errors

Claude tries to install packages and gets permission denied:

# npm: use --prefix or fix permissions
npm config set prefix ~/.npm-global
export PATH=~/.npm-global/bin:$PATH

# pip: use --user flag
# Tell Claude: "Use pip install --user when installing packages"

# Or use a virtual environment
python -m venv .venv
source .venv/bin/activate
# Then start Claude — it'll use the venv

Fix 6: Git permission errors

# "fatal: not a git repository"
# Initialize git first
git init
git add -A
git commit -m "Initial commit"

# "Permission denied (publickey)"
# Claude can't push to remote — this is expected
# Push manually after Claude makes changes
git push origin main

Claude Code works best in git repositories. It uses git for tracking changes and enabling /rewind. Always initialize git before starting a Claude session.

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