[BUG] IntelliJ plugin "Always Allow" button does not persist tool permissions to settings.json

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?

When using the Claude Code IntelliJ plugin on macOS, clicking "Always Allow" on a tool permission prompt does not persist the approval. The same tool is re-prompted on subsequent calls — even identical calls within the same conversation. This affects mutating tools (Write, Edit, Bash, WebSearch). The behavior is inconsistent for Bash: sometimes the same command is allowed without a prompt, sometimes it isn't, in the same session.

Manually adding entries to ~/.claude/settings.json resolves the issue, confirming that the plugin is not writing to (or not reliably writing to) this file when "Always Allow" is selected.

This may be related to #16762 (reported on Windows/PowerShell). This report adds the IntelliJ plugin on macOS as an additional affected environment.

What Should Happen?

Clicking "Always Allow" should persist the tool permission to ~/.claude/settings.json (or the appropriate project-level settings file), so subsequent calls to the same tool are not re-prompted.

Error Messages/Logs

No error messages. The ~/.claude/settings.json file remained {} after multiple "Always Allow" clicks across different tools.

Steps to Reproduce

1. Install the Claude Code IntelliJ plugin (beta) in IntelliJ IDEA on macOS
2. Open a project and start a Claude Code conversation
3. Ask Claude to write a file (e.g., Write tool to create tmp.txt)
4. When prompted, click "Always Allow"
5. Ask Claude to write the same file again
6. Observe: prompted again despite "Always Allow"
7. Check ~/.claude/settings.json — it remains {}
8. Manually add "permissions": {"allow": ["Write"]} to ~/.claude/settings.json
9. Repeat step 5 — no longer prompted

Claude Model

claude-opus-4-6

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

Claude Code via IntelliJ plugin (beta), March 2026

Platform

Anthropic API

Operating System

macOS (Darwin 25.3.0)

Terminal/Shell

zsh (via IntelliJ embedded terminal)

Additional Information

• Read-only tools (Read, Glob, Grep, Bash(ls), Bash(git status)) were never prompted, as expected.
• The intermittent behavior with Bash (same command sometimes prompted, sometimes not) suggests the approval state may be stored in memory but not reliably persisted or checked.
• See also #16762 for the same behavior on Windows/PowerShell.