[BUG] Workspace trust not persisting in Claude Code CLI - MCP servers fail to load despite accepting trust prompt

[laura-opendoor]

Preflight Checklist

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

What's Wrong?

Description:
When running Claude Code CLI from any directory, the workspace trust prompt appears and I select "Yes, proceed", but the trust decision is not persisted. This prevents MCP servers from loading in interactive sessions, even though they are properly configured and can connect successfully.

Environment:
OS: macOS (Darwin 25.1.0)
Claude Code CLI version: 2.0.50
Installation method: Native installer
Configuration location: ~/.claude/config.json

Steps to Reproduce:

1. Configure an MCP server in ~/.claude/config.json:
   {
   "mcpServers": {
   "snowflake": {
   "command": "/Users/laura/.local/bin/run_snowflake_mcp.sh"
   }
   }
   }

2. Run claude from home directory:
   cd ~
   claude

3. Trust prompt appears:
   Do you trust the files in this folder?
   /Users/laura

❯ 1. Yes, proceed
2. No, exit
Select "Yes, proceed"
Ask Claude to use MCP tools (e.g., query Snowflake)

Expected Behavior:
Trust decision should be saved/persisted
MCP servers should load in the session
MCP tools should be available (e.g., mcp__snowflake__*)

Actual Behavior:
Trust prompt is accepted but not persisted
On every new session, trust prompt appears again
MCP servers do not load in interactive sessions
Debug logs show: "workspace trust not accepted" even after accepting
MCP tools are not available in the session

Evidence:

1. MCP server CAN connect (outside of sessions):
   $ claude mcp list
   Checking MCP server health...
   snowflake: /Users/laura/.local/bin/mcp_snowflake_server - ✓ Connected

2. Debug logs show trust not accepted:
   From ~/.claude/debug/latest:
   2025-11-24T01:54:41.624Z [DEBUG] Skipping SessionStart:startup hook execution - workspace trust not accepted
   2025-11-24T01:54:41.646Z [DEBUG] Trust not accepted for current directory - skipping plugin installations

3. No MCP initialization attempts in logs:
   Searching for "mcp" or "MCP" in debug logs returns no results during session startup, indicating MCP servers are never being initialized when trust is not accepted.

4. No trust persistence:
   No trust-related keys found in ~/.claude.json
   Created test file at ~/.claude/workspaces/trusted.json but it's not being read
   Trust decision doesn't appear to be saved anywhere

What We've Tried:

1. Moving MCP server components outside workspace to avoid trust issues:
   Script: ~/.local/bin/run_snowflake_mcp.sh
   Virtual env: ~/.local/mcp-servers/snowflake/.venv/
   Credentials: ~/.config/snowflake/mcp.env

2. Updated settings in ~/.claude/settings.local.json:
   {
   "permissions": {
   "allow": ["mcp__snowflake__*"],
   "defaultMode": "dontAsk"
   },
   "enableAllProjectMcpServers": true
   }

3. Manually created trust file at ~/.claude/workspaces/trusted.json:
   {
   "trustedWorkspaces": ["/Users/laura", "/Users/laura/monorepo"]
   }
   → Not being read/used

Additional Context:
This happens from any directory (home, monorepo, /tmp, etc.)
The trust prompt appears every single session
Accepting trust has no effect - logs still show "workspace trust not accepted"
The -p (print mode) flag mentions trust is skipped, confirming trust is intentionally checked in interactive mode

Workaround:
Using VSCode extension instead of CLI, which doesn't have this trust persistence issue.

Impact:
MCP servers are completely unusable in Claude Code CLI interactive sessions due to workspace trust not persisting, despite proper configuration.

What Should Happen?

Expected Behavior:
Trust decision should be saved/persisted
MCP servers should load in the session
MCP tools should be available (e.g., mcp__snowflake__*)

Error Messages/Logs

**Actual Behavior:**
Trust prompt is accepted but not persisted
On every new session, trust prompt appears again
MCP servers do not load in interactive sessions
Debug logs show: "workspace trust not accepted" even after accepting
MCP tools are not available in the session

Steps to Reproduce

Steps to Reproduce:

1. Configure an MCP server in ~/.claude/config.json:
   {
   "mcpServers": {
   "snowflake": {
   "command": "/Users/laura/.local/bin/run_snowflake_mcp.sh"
   }
   }
   }

2. Run claude from home directory:
   cd ~
   claude

3. Trust prompt appears:
   Do you trust the files in this folder?
   /Users/laura

❯ 1. Yes, proceed
2. No, exit
Select "Yes, proceed"
Ask Claude to use MCP tools (e.g., query Snowflake)

Claude Model

None

Is this a regression?

I don't know

Last Working Version

No response

Claude Code Version

Claude Code CLI version: 2.0.50

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

No response

[github-actions]

Found 3 possible duplicate issues:

1. Bug: PreToolUse Hooks Skipped - "Workspace Trust Not Accepted" #12100
2. [BUG] Workspace Trust Dialog Not Respecting Pre-configured ~/.claude/.claude.json #9113
3. [BUG] Using dangerously-skip-permissions on a new folder skips trust check and breaks hooks #10409

This issue will be automatically closed as a duplicate in 3 days.

• If your issue is a duplicate, please close it and 👍 the existing issue instead
• To prevent auto-closure, add a comment or 👎 this comment

🤖 Generated with Claude Code

[laura-opendoor]

Found 3 possible duplicate issues:

1. Bug: PreToolUse Hooks Skipped - "Workspace Trust Not Accepted" #12100
2. [BUG] Workspace Trust Dialog Not Respecting Pre-configured ~/.claude/.claude.json #9113
3. [BUG] Using dangerously-skip-permissions on a new folder skips trust check and breaks hooks #10409

This issue will be automatically closed as a duplicate in 3 days.

• If your issue is a duplicate, please close it and 👍 the existing issue instead
• To prevent auto-closure, add a comment or 👎 this comment

🤖 Generated with Claude Code

The bugs listed are related to trust issues, but none address my particular issue that even when I confirm trust, that confirmation is not saved, not even for the single session that I am in. Thus, Claude thinks I did not confirm trust when I did, and is thus not allowing mcp_snowflake_server to start.

[laura-opendoor]

Checking in on this bug. Please provide an update. Thanks.

[github-actions]

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.