[BUG] Bypass permissions not working in Antigravity/VS Code Remote SSH despite all configurations (v2.1.73)

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?

Issue Body:

Bug Description

The bypass permissions mode does not work in the Antigravity/VS Code extension when using Remote SSH connections, despite having all recommended configurations in place. Permission prompts still appear for every tool use.

Environment

• Claude Code Version: 2.1.73
• IDE: Antigravity (Anthropic's VS Code fork)
• Connection Type: Remote SSH
• Remote OS: Ubuntu 24.04.3 LTS (GNU/Linux 6.14.0-37-generic x86_64)
• Local OS: Windows
• Extension: anthropic.claude-code-2.1.73-linux-x64

Configuration Attempted

1. VS Code Settings (Machine-level)

Location: ~/.antigravity-server/data/Machine/settings.json

{
    "claudeCode.initialPermissionMode": "bypassPermissions",
    "claudeCode.preferredLocation": "sidebar",
    "claudeCode.allowDangerouslySkipPermissions": true,
    "claudeCode.disableLoginPrompt": true,
    "claudeCode.environmentVariables": []
}
2. Claude Settings
Location: ~/.claude/settings.json
{
  "permissions": {
    "allow": ["*"],
    "defaultMode": "bypassPermissions"
  },
  "hooks": {
    "PreToolUse": [
      {
        "hooks": [
          {
            "type": "command",
            "command": "/home/hamed/.claude/hooks/pre-tool-use.sh"
          }
        ]
      }
    ]
  }
}
3. PreToolUse Hook
Location: ~/.claude/hooks/pre-tool-use.sh
#!/bin/bash
# Auto-approve all tool uses
TOOL_CALL=$(cat)

cat <<EOF
{
  "hookSpecificOutput": {
    "hookEventName": "PermissionRequest",
    "decision": {
      "behavior": "allow"
    }
  }
}
EOF
4. Additional Configurations Tried
✅ AntiGravity AutoAccept extension installed (v3.9.13)
✅ Chrome DevTools Protocol enabled (--remote-debugging-port=9333)
✅ Wildcard allow: ["*"]
✅ Explicit tool permissions (Bash, Write, Read, etc.)
✅ Multiple VS Code reloads
✅ Extension updated to latest version
Expected Behavior
With claudeCode.allowDangerouslySkipPermissions: true and defaultMode: "bypassPermissions", the extension should bypass all permission prompts automatically.
Actual Behavior
Permission prompts still appear for every single tool use (Bash, Write, Edit, etc.), requiring manual approval each time:
Allow this bash command?
echo "Testing permissions - $(date)"

1 Yes
2 No
Steps to Reproduce
Install Claude Code extension v2.1.73 in Antigravity
Connect to a remote server via SSH
Configure all settings as shown above
Start a Claude Code session
Execute any tool (Bash, Write, etc.)
Result: Permission prompt still appears
Related Issues
This appears related to:
#20536 - bypassPermissions mode not working in VS Code extension
#12604 - VSCode Extension: Permission settings not working
#29159 - VSCode extension does not enforce permissions from settings.json
Notes
The CLI version with claude --dangerously-skip-permissions works correctly
The issue is specific to VS Code/Antigravity Remote SSH connections
Settings files ARE being read (verified with test values)
The hook is NOT being executed (no logs, no auto-approval)
Question
Is there a known working configuration for bypass permissions in Remote SSH environments? Or is this functionality currently broken in the VS Code extension?
Workaround Needed
Currently having to manually click "Yes" on every single permission prompt, which significantly impacts productivity.

### What Should Happen?

Expected Behavior
With claudeCode.allowDangerouslySkipPermissions: true and defaultMode: "bypassPermissions", the extension should bypass all permission prompts automatically.
Actual Behavior
Permission prompts still appear for every single tool use (Bash, Write, Edit, etc.), requiring manual approval each time:
Allow this bash command?
echo "Testing permissions - $(date)"

1 Yes
2 No
Steps to Reproduce
Install Claude Code extension v2.1.73 in Antigravity
Connect to a remote server via SSH
Configure all settings as shown above
Start a Claude Code session
Execute any tool (Bash, Write, etc.)
Result: Permission prompt still appears
Related Issues
This appears related to:
#20536 - bypassPermissions mode not working in VS Code extension
#12604 - VSCode Extension: Permission settings not working
#29159 - VSCode extension does not enforce permissions from settings.json
Notes
The CLI version with claude --dangerously-skip-permissions works correctly
The issue is specific to VS Code/Antigravity Remote SSH connections
Settings files ARE being read (verified with test values)
The hook is NOT being executed (no logs, no auto-approval)
Question
Is there a known working configuration for bypass permissions in Remote SSH environments? Or is this functionality currently broken in the VS Code extension?

### Error Messages/Logs

```shell
Issue Body:
## Bug Description

The bypass permissions mode does not work in the Antigravity/VS Code extension when using Remote SSH connections, despite having all recommended configurations in place. Permission prompts still appear for every tool use.

## Environment

- **Claude Code Version:** 2.1.73
- **IDE:** Antigravity (Anthropic's VS Code fork)
- **Connection Type:** Remote SSH
- **Remote OS:** Ubuntu 24.04.3 LTS (GNU/Linux 6.14.0-37-generic x86_64)
- **Local OS:** Windows
- **Extension:** anthropic.claude-code-2.1.73-linux-x64

## Configuration Attempted

### 1. VS Code Settings (Machine-level)
Location: `~/.antigravity-server/data/Machine/settings.json`


{
    "claudeCode.initialPermissionMode": "bypassPermissions",
    "claudeCode.preferredLocation": "sidebar",
    "claudeCode.allowDangerouslySkipPermissions": true,
    "claudeCode.disableLoginPrompt": true,
    "claudeCode.environmentVariables": []
}
2. Claude Settings
Location: ~/.claude/settings.json
{
  "permissions": {
    "allow": ["*"],
    "defaultMode": "bypassPermissions"
  },
  "hooks": {
    "PreToolUse": [
      {
        "hooks": [
          {
            "type": "command",
            "command": "/home/hamed/.claude/hooks/pre-tool-use.sh"
          }
        ]
      }
    ]
  }
}
3. PreToolUse Hook
Location: ~/.claude/hooks/pre-tool-use.sh
#!/bin/bash
# Auto-approve all tool uses
TOOL_CALL=$(cat)

cat <<EOF
{
  "hookSpecificOutput": {
    "hookEventName": "PermissionRequest",
    "decision": {
      "behavior": "allow"
    }
  }
}
EOF
4. Additional Configurations Tried
✅ AntiGravity AutoAccept extension installed (v3.9.13)
✅ Chrome DevTools Protocol enabled (--remote-debugging-port=9333)
✅ Wildcard allow: ["*"]
✅ Explicit tool permissions (Bash, Write, Read, etc.)
✅ Multiple VS Code reloads
✅ Extension updated to latest version
Expected Behavior
With claudeCode.allowDangerouslySkipPermissions: true and defaultMode: "bypassPermissions", the extension should bypass all permission prompts automatically.
Actual Behavior
Permission prompts still appear for every single tool use (Bash, Write, Edit, etc.), requiring manual approval each time:
Allow this bash command?
echo "Testing permissions - $(date)"

1 Yes
2 No
Steps to Reproduce
Install Claude Code extension v2.1.73 in Antigravity
Connect to a remote server via SSH
Configure all settings as shown above
Start a Claude Code session
Execute any tool (Bash, Write, etc.)
Result: Permission prompt still appears
Related Issues
This appears related to:
#20536 - bypassPermissions mode not working in VS Code extension
#12604 - VSCode Extension: Permission settings not working
#29159 - VSCode extension does not enforce permissions from settings.json
Notes
The CLI version with claude --dangerously-skip-permissions works correctly
The issue is specific to VS Code/Antigravity Remote SSH connections
Settings files ARE being read (verified with test values)
The hook is NOT being executed (no logs, no auto-approval)
Question
Is there a known working configuration for bypass permissions in Remote SSH environments? Or is this functionality currently broken in the VS Code extension?
Workaround Needed
Currently having to manually click "Yes" on every single permission prompt, which significantly impacts productivity.

Steps to Reproduce

Install Claude Code extension v2.1.73 in Antigravity
Connect to a remote server via SSH
Configure all settings as shown above
Start a Claude Code session
Execute any tool (Bash, Write, etc.)
Result: Permission prompt still appears

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.73

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_