`~/.mcp.json` is not a user-scope MCP location, so the documented setup silently fails

[e-q]

README.md:380-385 describes ~/.mcp.json as "global servers available in every session." There is no such location.

MCP user scope lives in ~/.claude.json. A file at ~/.mcp.json is only picked up incidentally, as a project-scope .mcp.json discovered by walking up the directory tree from the working directory — which happens to work for repos under $HOME and nowhere else.

Two consequences:

• Because it resolves as project scope, it's gated by the project-server approval flow — and this repo's settings.json sets enableAllProjectMcpServers: false. The README's two recommendations work against each other.
• For anyone who keeps repos outside $HOME, the servers silently don't load at all.

Verified

macOS, CLI 2.1.238, with ~/.mcp.json present and populated from mcp-template.json:

$ cd ~/Developer/claude-code-config && claude mcp get exa
exa:
  Scope: Project config (shared via .mcp.json)
  Status: ⏸ Pending approval (run `claude` to approve)
  Type: http

$ cd /private/tmp/scratch && claude mcp get exa
No MCP server named "exa".

The Scope: Project config line and the pending-approval status are both the symptom: it was never registered as a user-scope server.

Suggested fix

Drop ~/.mcp.json from the README and from /trailofbits:config, and use the CLI, which writes real user scope:

claude mcp add --transport http exa --scope user 'https://mcp.exa.ai/mcp' --header "x-api-key: $EXA_API_KEY"
claude mcp add context7 --scope user -- npx -y @upstash/context7-mcp

That leaves mcp-template.json without a purpose — either remove it, or relabel it as an example project-scoped .mcp.json rather than something to copy into $HOME.

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Found while reviewing the repo against Anthropic's current docs and the installed CLI (2.1.238). One of five separate findings from the same pass.