[BUG] --permission-mode bypassPermissions / --dangerously-skip-permissions not working in print mode (-p) with --resume

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Bug Title: --permission-mode bypassPermissions not working with --resume

Version: 2.1.79 CC

Description:
The Write tool is being blocked when using --resume with --permission-mode bypassPermissions, even for paths that should be exempt.

Steps to Reproduce:

Start a session with --permission-mode bypassPermissions
Resume the session using --resume <session_id> --permission-mode bypassPermissions
Attempt to write to .claude/skills/ directory
Expected Behavior:
Writes to .claude/skills/ should succeed without prompting, per documentation: "Writes to .claude/commands, .claude/agents, and .claude/skills are exempt and do not prompt."

Actual Behavior:
Write tool is blocked with permission_denials:

{
"tool_name": "Write",
"file_path": "C:\\Demo Projects\\ai-human-collab-framework\\.claude\\skills\\basic-test-skill\\SKILL.md"
}
Environment: Windows

What Should Happen?

CC should proceed as per instructions

Error Messages/Logs

Steps to Reproduce

see issue details

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.79

Platform

Other

Operating System

Windows

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_

Key details to include:

Using -p (print mode) + --output-format json
--permission-mode bypassPermissions passed with --resume
Write tool still blocked, Claude waiting for approval that can't be given in non-interactive mode
This is likely a regression or edge case not yet fixed.