MCP servers from .mcp.json not visible in session despite CLI showing them connected

Description

MCP servers configured in a project-level .mcp.json are not visible or usable in active sessions, even though claude mcp list from the CLI confirms they are all connected.

Steps to reproduce

1. Have a project-level .mcp.json with multiple MCP servers configured (mix of stdio and http types)
2. Start a Claude Code session in the project directory
3. Run /mcp in the session — only a subset of servers appear (in my case, only sentry plus claude.ai built-in integrations)
4. Run claude mcp list from the terminal — all servers show as ✓ Connected

Expected behavior

All connected MCP servers should appear in the /mcp dialog and their tools should be available in the session.

Actual behavior

/mcp only shows sentry, claude.ai, and the claude.ai-provided integrations (Gmail, Google Calendar, HubSpot). The following servers are invisible in the session despite claude mcp list confirming they are connected:

• ag-mcp (stdio)
• angular-cli (stdio)
• github (http with Bearer token)
• nx-mcp (stdio)
• primeng (stdio)
• wallaby (stdio)
• circleci-mcp-server (stdio)
• figma-remote-mcp (http, needs auth — expected to not work, but should still appear)

Environment

• Claude Code version: 2.1.87
• OS: macOS (Darwin 25.4.0)
• Shell: zsh

.mcp.json (redacted)

{
  "mcpServers": {
    "ag-mcp": { "type": "stdio", "command": "npx", "args": ["ag-mcp"] },
    "angular-cli": { "command": "npx", "args": ["-y", "@angular/cli", "mcp"] },
    "github": { "type": "http", "url": "https://api.githubcopilot.com/mcp", "headers": { "Authorization": "Bearer ${GITHUB_PAT}" } },
    "nx-mcp": { "type": "stdio", "command": "npx", "args": ["nx", "mcp"] },
    "primeng": { "type": "stdio", "command": "npx", "args": ["-y", "@primeng/mcp"] },
    "sentry": { "type": "http", "url": "https://mcp.sentry.dev/mcp" },
    "wallaby": { "type": "stdio", "command": "npx", "args": ["-y", "-c", "node ~/.wallaby/mcp"] },
    "circleci-mcp-server": { "type": "stdio", "command": "npx", "args": ["-y", "@circleci/mcp-server-circleci@latest"] },
    "figma-remote-mcp": { "type": "http", "url": "https://mcp.figma.com/mcp" }
  }
}

claude mcp list output

claude.ai Google Calendar: https://gcal.mcp.claude.com/mcp - ✓ Connected
claude.ai Gmail: https://gmail.mcp.claude.com/mcp - ✓ Connected
claude.ai HubSpot: https://mcp.hubspot.com/anthropic - ✓ Connected
ag-mcp: npx ag-mcp - ✓ Connected
angular-cli: npx -y @angular/cli mcp - ✓ Connected
github: https://api.githubcopilot.com/mcp (HTTP) - ✓ Connected
nx-mcp: npx nx mcp - ✓ Connected
primeng: npx -y @primeng/mcp - ✓ Connected
sentry: https://mcp.sentry.dev/mcp (HTTP) - ✓ Connected
wallaby: npx -y -c node ~/.wallaby/mcp - ✓ Connected
circleci-mcp-server: npx -y @circleci/mcp-server-circleci@latest - ✓ Connected
figma-remote-mcp: https://mcp.figma.com/mcp (HTTP) - ! Needs authentication

Additional context

• This persists across session restarts
• Also tried adding the github server to ~/.claude/mcp.json (user-level) — same result, did not appear in session
• The GITHUB_PAT env var is set and available in the shell
• The servers were previously working in earlier sessions