VSCode Extension: Permissions not persisting

Area - Claude Code, CLI, Windows, Mac OS

This is my problem too: my allow section looks like this:

{
  "permissions": {
    "allow": [
      "Bash(git *)",
      "Bash(poetry *)",
      "Bash(DJANGO_ENV=* poetry *)",
      "Bash(TEST_ENV=* *)",
      "Bash(python *)",
      "Bash(node *)",
      "Bash(npm *)",
      "Bash(npx *)",
      "Bash(powershell *)",
      "Bash(cmd *)",
      "Bash(mkdir *)",
      "Bash(rmdir *)",
      "Bash(del *)",
      "Bash(rm *)",
      "Bash(cp *)",
      "Bash(mv *)",
      "Bash(move *)",
      "Bash(copy *)",
      "Bash(cat *)",
      "Bash(echo *)",
      "Bash(dir *)",
      "Bash(ls *)",
      "Bash(tree *)",
      "Bash(find *)",
      "Bash(findstr *)",
      "Bash(grep *)",
      "Bash(curl *)",
      "Bash(wget *)",
      "Bash(timeout *)",
      "Bash(ping *)",
      "Bash(netstat *)",
      "Bash(tasklist *)",
      "Bash(taskkill *)",
      "Bash(test *)",
      "Bash(touch *)",
      "Bash(tee *)",
      "Bash(cut *)",
      "Bash(xargs *)",
      "Bash(bash *)",
      "Bash(sh *)",
      "Bash(if *)",
      "Bash(for *)",
      "Bash(while *)",
      "Bash(time *)",
      "Bash(export *)",
      "Bash(*)",
      "WebSearch",
      "WebFetch(*)"
    ],
    "deny": [],
    "ask": []
  },
  "outputStyle": "default",
  "spinnerTipsEnabled": false
}

WHEN I ask for commit
THEN Claude asks me for git commit approval.
AND
THEN all the "allow" section gets wiped out (no entries at all)
THEN new entry is created with this specific command just approved

All I need to get is Claude Code working with all the tools it needs - the environment is controlled, it can REALLY do whatever it needs, I want it to get all approvals once for good and forget this topic.

I'm experiencing this too, but in cli with the sandbox enabled. Here's what the agent an I worked out together:

Tested on: Claude Code CLI version 2.0.58

Discovery
Project-level .claude/settings.json or .claude/settings.local.json that contain ANY sandbox section will completely override (not merge
with) all user-level sandbox settings from ~/.claude/settings.json.

### What This Means

If you have:

• User settings (~/.claude/settings.json) with sandbox.filesystem.write.allowOnly paths
• Project settings (.claude/settings.local.json) with ANY sandbox configuration

Result: All user-level sandbox paths are completely ignored. The settings are not additive - project settings replace user settings entirely.

### Why This Matters

This creates a confusing situation where:

1. Users configure sandbox paths in user settings
2. Project adds a sandbox section (even just "sandbox": { "enabled": true })
3. All user-level paths stop working
4. Writes fail with "Read-only file system" despite being in user allowOnly
5. No indication that project settings are overriding user settings

### Expected Behavior

Settings should be additive/merged:

• User settings provide system-wide defaults
• Project settings add project-specific paths
• Combined allowOnly list = user paths + project paths

### Actual Behavior

Settings are replaced:

• If project has sandbox section, it completely replaces user sandbox section
• User paths are lost entirely
• No warning or indication this is happening

This issue has been inactive for 30 days. If the issue is still occurring, please comment to let us know. Otherwise, this issue will be automatically closed in 30 days for housekeeping purposes.

Since a bug can't solve itself, I assume this is still occurring.
Since it is annoying to have this bug, I don't use the extension.

Yup still happening. Related to #15772

This issue has been automatically closed due to 60 days of inactivity. If you're still experiencing this issue, please open a new issue with updated information.

This issue was closed incorrectly despite recent human comments. This behavior of the bot is reported at https://github.com/anthropics/claude-code/issues/16497. Please upvote that issue, so maybe it gets noticed.

This issue has been automatically locked since it was closed and has not had any activity for 7 days. If you're experiencing a similar issue, please file a new issue and reference this one if it's relevant.