--strict-mcp-config does not override disabledMcpServers

Description

The --strict-mcp-config flag does not override the disabledMcpServers list stored in ~/.claude.json. This makes the flag unusable for its intended purpose of loading a custom MCP configuration that ignores all other settings.

Expected Behavior

According to the docs, --strict-mcp-config should "only use MCP servers from --mcp-config, ignoring all other MCP configurations." The disabledMcpServers setting should be part of "all other MCP configurations" and therefore ignored.

Actual Behavior

MCP servers listed in disabledMcpServers for a project remain disabled even when:

1. Using --mcp-config to load a config containing that server
2. Using --strict-mcp-config to ignore all other configurations
3. Passing the MCP config as an inline JSON string

Reproduction Steps

1. Have a project with an MCP server (e.g., "axiom") in disabledMcpServers in ~/.claude.json
2. Run: e.g. claude --strict-mcp-config --mcp-config '{"mcpServers":{"axiom":{"type":"stdio","command":"npx","args":["-y","mcp-remote","https://mcp.axiom.co/mcp"]}}}'
3. Observe that axiom is still disabled

Environment

• Claude Code version: 2.0.72
• OS: macOS Darwin 24.3.0

Workaround

Manually edit ~/.claude.json to remove the server from disabledMcpServers, which defeats the purpose of having CLI flags for temporary/debug configurations.