[BUG] Permission Request Prompts with --dangerously-skip-permissions

Environment

• Claude CLI version: 1.0.77
• Host OS: MacOS 15.6
• Container OS: Debian GNU/Linux 12

Bug Description

Seeing permission prompts when running Claude Code with --dangerously-skip-permissions.

It occurs during a large task.

Minimal Reproduction

I can force a reproduction of the issue:

> list dir /

● I'll list the contents of the root directory for you.

● List(/)

╭─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ Read file                                                                                                                                                                       │
│                                                                                                                                                                                 │
│   List(/)                                                                                                                                                                       │
│                                                                                                                                                                                 │
│ Do you want to proceed?                                                                                                                                                         │
│ ❯ 1. Yes                                                                                                                                                                        │
│   2. Yes, and add / as a working directory for this session                                                                                                                     │
│   3. No, and tell Claude what to do differently (esc)                                                                                                                           │
│                                                                                                                                                                                 │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

Additional Context & Settings

I am running Claude Code in a container.

The settings.json:

{
  "permissions": {
    "defaultMode": "bypassPermissions",
    "allow": [
      "Bash(*)",
      "Edit(*)",
      "Glob(*)",
      "Grep(*)",
      "LS(*)",
      "List(*)",
      "List(..)",
      "MultiEdit(*)",
      "NotebookEdit(*)",
      "NotebookRead(*)",
      "Read(*)",
      "Task(*)",
      "TodoWrite(*)",
      "WebFetch(*)",
      "WebSearch(*)",
      "Write(*)"
    ],
    "deny": [],
    "additionalDirectories": ["/", "/workspace", "/home", "/etc", "/usr", "/var", "/tmp", "/root", "../"]
  }
}`

The container has the following env variables set:

CLAUDE_CODE_BYPASS_ALL_PERMISSIONS=1
CLAUDE_CODE_SUPPRESS_UI_PROMPTS=1
ANTHROPIC_DISABLE_SAFETY_CHECKS=1
CLAUDE_CODE_ENTERPRISE_MODE=1
DISABLE_AUTOUPDATER=1
CLAUDE_CODE_ENABLE_TELEMETRY=0
CLAUDE_WORKING_DIRECTORIES="/workspace:/workspace/..:/:/home:/etc:/usr:/var:/tmp:/root"

Claude Code is launched inside of the container with:

claude --dangerously-skip-permissions

Inside of the container, running:

> /status
...
 Working Directory
  L /workspace
...

Attempting to explicitly add to the working directories in the current session does not appear to work:

> /add-dir /
  ⎿  / is already accessible within the existing working directory /.

> list dir /

● List(/)

╭─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ Read file                                                                                                                                                                       │
│                                                                                                                                                                                 │
│   List(/)                                                                                                                                                                       │
│                                                                                                                                                                                 │
│ Do you want to proceed?                                                                                                                                                         │
│ ❯ 1. Yes                                                                                                                                                                        │
│   2. Yes, and add / as a working directory for this session                                                                                                                     │
│   3. No, and tell Claude what to do differently (esc)                                                                                                                           │
│                                                                                                                                                                                 │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯