[Bug] Permission mode "auto" not inherited in new sessions and cannot be set mid-session

Bug Description
Title: auto permission mode not inherited by new sessions and cannot be set mid-session

Product: Claude Code Desktop (Windows)
defaultMode setting: "auto" in ~/.claude/settings.json

SUMMARY
When defaultMode is set to "auto" in ~/.claude/settings.json, new Claude Code sessions do not inherit it. The session appears to start in auto mode but switches to "default" (ask-every-time) after the first message. Additionally, clicking auto mode in the permission selector mid-session causes the UI to immediately flip back to the previous mode — auto cannot be set at all during that session.

This does NOT occur with defaultMode: "bypassPermissions" — that value is correctly inherited by all new sessions and persists without issue.

STEPS TO REPRODUCE

1. Set permissions.defaultMode: "auto" in ~/.claude/settings.json
2. Set skipAutoPermissionPrompt: true
3. Restart Claude Desktop
4. Open a new Claude Code session
5. Send one message
6. Check the permission mode indicator

Expected: Session stays in auto mode
Actual: Session switches to "default" after first message

1. Click the permission selector and choose "auto"

Expected: Mode switches to auto and stays
Actual: Mode immediately flips back — auto cannot be set mid-session

OBSERVED SESSION STATE
Per-session state files at:
C:/Users/[user]/AppData/Roaming/Claude/claude-code-sessions/[account-uuid]/[workspace-uuid]/[session-id].json

Each file has a permissionMode field. With defaultMode: "bypassPermissions", all session files correctly show permissionMode: bypassPermissions. With defaultMode: "auto", new session files show permissionMode: default instead — the global default is being ignored specifically for the "auto" value.

ENVIRONMENT

• OS: Windows 11
• Claude Desktop, auto-updates enabled (latest channel)
• skipAutoPermissionPrompt: true
• skipDangerousModePermissionPrompt: true

HYPOTHESIS
There may be a validation or normalisation step that strips "auto" when writing the per-session state file after the first turn. Worth checking the code path that writes permissionMode to the session JSON on first message completion.

Environment Info

• Platform: win32
• Terminal: null
• Version: 2.1.77
• Feedback ID: 23374772-748a-4920-99b5-09f2cbc8b181

Errors

[{"error":"Error: Plugin path not found: C:\\Users\\Robbie\\.claude\\plugins\\marketplaces\\claude-plugins-official\\external_plugins\\autofix-bot\n    at AU1 (B:/~BUN/root/src/entrypoints/cli.js:2525:8003)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-02T11:20:31.397Z"},{"error":"Error: Plugin MCP server error - mcp-config-invalid: MCP server github invalid: Missing environment variables: GITHUB_PERSONAL_ACCESS_TOKEN\n    at FEH (B:/~BUN/root/src/entrypoints/cli.js:2532:32833)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-02T11:20:31.482Z"},{"error":"Error: Plugin MCP server error - mcp-config-invalid: MCP server github invalid: Missing environment variables: GITHUB_PERSONAL_ACCESS_TOKEN\n    at FEH (B:/~BUN/root/src/entrypoints/cli.js:2532:32833)\n    at async X (B:/~BUN/root/src/entrypoints/cli.js:4860:17025)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-02T11:21:17.906Z"},{"error":"Error: Plugin MCP server error - mcp-config-invalid: MCP server github invalid: Missing environment variables: GITHUB_PERSONAL_ACCESS_TOKEN\n    at FEH (B:/~BUN/root/src/entrypoints/cli.js:2532:32833)\n    at async G (B:/~BUN/root/src/entrypoints/cli.js:4860:17741)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-05-02T11:21:17.907Z"}]