[BUG] --bare mode loads user configuration

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 running claude with the --bare flag, it loads the MCP servers i have configured in ~/.claude/settings.json, but i expected it not to.

What Should Happen?

From the documentation i believe this is a bug: https://code.claude.com/docs/en/headless#start-faster-with-bare-mode:
"Add --bare to reduce startup time by skipping auto-discovery of hooks, skills, plugins, MCP servers, auto memory, and CLAUDE.md."

i expect the system message NOT to include mcp servers from my user folder (or any other folder for that matter)

Error Messages/Logs

System message:

{
    "type": "system",
    "subtype": "init",
    "cwd": "<a folder inside an existing project>",
    "session_id": "64207866-89c5-47f3-873b-0e17490852fc",
    "tools": [
        "Bash",
        "Edit",
        "ListMcpResourcesTool",
        "mcp__azureDevOps__add_pull_request_comment",
        "mcp__azureDevOps__create_branch",
        "mcp__azureDevOps__create_commit",
        "mcp__azureDevOps__create_pull_request",
        "mcp__azureDevOps__create_wiki",
        "mcp__azureDevOps__create_wiki_page",
        "mcp__azureDevOps__create_work_item",
        "mcp__azureDevOps__download_pipeline_artifact",
        "mcp__azureDevOps__get_all_repositories_tree",
        "mcp__azureDevOps__get_file_content",
        "mcp__azureDevOps__get_me",
        "mcp__azureDevOps__get_pipeline",
        "mcp__azureDevOps__get_pipeline_log",
        "mcp__azureDevOps__get_pipeline_run",
        "mcp__azureDevOps__get_project",
        "mcp__azureDevOps__get_project_details",
        "mcp__azureDevOps__get_pull_request",
        "mcp__azureDevOps__get_pull_request_changes",
        "mcp__azureDevOps__get_pull_request_checks",
        "mcp__azureDevOps__get_pull_request_comments",
        "mcp__azureDevOps__get_repository",
        "mcp__azureDevOps__get_repository_details",
        "mcp__azureDevOps__get_repository_tree",
        "mcp__azureDevOps__get_wiki_page",
        "mcp__azureDevOps__get_wikis",
        "mcp__azureDevOps__get_work_item",
        "mcp__azureDevOps__list_commits",
        "mcp__azureDevOps__list_organizations",
        "mcp__azureDevOps__list_pipeline_runs",
        "mcp__azureDevOps__list_pipelines",
        "mcp__azureDevOps__list_projects",
        "mcp__azureDevOps__list_pull_requests",
        "mcp__azureDevOps__list_repositories",
        "mcp__azureDevOps__list_wiki_pages",
        "mcp__azureDevOps__list_work_items",
        "mcp__azureDevOps__manage_work_item_link",
        "mcp__azureDevOps__pipeline_timeline",
        "mcp__azureDevOps__search_code",
        "mcp__azureDevOps__search_wiki",
        "mcp__azureDevOps__search_work_items",
        "mcp__azureDevOps__trigger_pipeline",
        "mcp__azureDevOps__update_pull_request",
        "mcp__azureDevOps__update_wiki_page",
        "mcp__azureDevOps__update_work_item",
        "mcp__rider__create_new_file",
        "mcp__rider__execute_run_configuration",
        "mcp__rider__execute_terminal_command",
        "mcp__rider__find_files_by_glob",
        "mcp__rider__find_files_by_name_keyword",
        "mcp__rider__get_all_open_file_paths",
        "mcp__rider__get_file_problems",
        "mcp__rider__get_file_text_by_path",
        "mcp__rider__get_project_dependencies",
        "mcp__rider__get_project_modules",
        "mcp__rider__get_repositories",
        "mcp__rider__get_run_configurations",
        "mcp__rider__get_symbol_info",
        "mcp__rider__list_directory_tree",
        "mcp__rider__open_file_in_editor",
        "mcp__rider__permission_prompt",
        "mcp__rider__reformat_file",
        "mcp__rider__rename_refactoring",
        "mcp__rider__replace_text_in_file",
        "mcp__rider__search_in_files_by_regex",
        "mcp__rider__search_in_files_by_text",
        "Read",
        "ReadMcpResourceTool"
    ],
    "mcp_servers": [
        {
            "name": "azureDevOps",
            "status": "connected"
        },
        {
            "name": "rider",
            "status": "connected"
        }
    ],
    "model": "claude-sonnet-4-6[1m]",
    "permissionMode": "default",
    "slash_commands": [
        "update-config",
        "debug",
        "simplify",
        "batch",
        "loop",
        "schedule",
        "claude-api",
        "compact",
        "context",
        "cost",
        "heapdump",
        "init",
        "pr-comments",
        "release-notes",
        "review",
        "security-review",
        "insights"
    ],
    "apiKeySource": "ANTHROPIC_API_KEY",
    "claude_code_version": "2.1.83",
    "output_style": "default",
    "agents": [
        "general-purpose",
        "statusline-setup",
        "Explore",
        "Plan"
    ],
    "skills": [
        "update-config",
        "debug",
        "simplify",
        "batch",
        "loop",
        "schedule",
        "claude-api"
    ],
    "plugins": [],
    "uuid": "3760f5f7-33db-4eda-8703-035b69a92aff",
    "fast_mode_state": "off"
}

Steps to Reproduce

In powershell run:
claude --bare -p "whats 2+2?" --output-format json-stream
the output clearly shows the mcp servers being included in the system message, both in the tools array and the mcp_servers array.

i have tried various combinations of cli params and env vars with the same result
claude -p --bare "whats 2+2?" --output-format json-stream

$env:CLAUDE_CODE_SIMPLE = 1
claude -p --bare "whats 2+2?" --output-format json-stream

I tried providing a json file as the mcpconfig, with no mcp servers configured, with the same result
mcpServers.json => {"mcpServers": {}}
claude -p --bare "whats 2+2?" --output-format json-stream --mcp-config ./mcpServers.json

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.83 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

_No response_