feat: add generic kernel-owned MCP runtime

[sethkarten]

Summary

• add the pre-imported mcp.list_tools(server) and mcp.call_tool(server, tool, arguments) API for user-configured MCP servers
• keep one initialized kernel-owned generation per server, with discovery-before-ready, serialized replacement, bounded startup/call/close, cancellation, and tool filters at listing and dispatch
• support anonymous/bearer/static-header/existing-OAuth Streamable HTTP and argv-only stdio with tagged environment references and scrubbed ambient environment
• ignore project-local MCP declarations for execution while preserving authored Linear and Notion wrappers

Tests

• cd prime-agent-runtime && uv run --with pytest python -m pytest -q test (74 passed; includes real keyless stdio and Streamable HTTP fixtures)
• cd packages/coding-agent && npx tsx ../../node_modules/vitest/dist/cli.js --run test/mcp-manager.test.ts test/settings-manager.test.ts test/ipython-bootstrap.test.ts test/kernel-bootstrap.test.ts (77 passed)
• cd packages/coding-agent && unset RLM_DEPTH RLM_MAX_DEPTH && npx tsx ../../node_modules/vitest/dist/cli.js --run test/agent-session-recursion.test.ts (96 passed)
• cd packages/coding-agent && npx tsx ../../node_modules/vitest/dist/cli.js --run test/kernel-startup.test.ts test/kernel-abort.test.ts (6 passed)
• npm run check
• git diff --check

---

Note

High Risk
Touches kernel bootstrap, subprocess stdio MCP, credential handling, and global settings persistence; outdated kernels without the new runtime will fail readiness checks.

Overview
Adds a kernel-owned generic MCP client (rlm.mcp) with list_tools, call_tool, reload, and close, supporting Streamable HTTP and stdio transports, per-server connection reuse, startup/call timeouts, tool allow/deny filters, and redacted stdio startup diagnostics.

CLI and TUI can persist user MCP servers via mcp add|list|get|remove (and /mcp equivalents). Entries live only in global ~/.prime/agent/settings.json; project MCP configs are no longer used for execution. Stdio secrets are env-var references only; list/get output shows name and transport, not commands or tokens.

The system prompt advertises enabled generic servers and await mcp.list_tools / await mcp.call_tool when IPython is active. Kernel bootstrap now requires callable mcp.list_tools and mcp.call_tool. Catalog names (e.g. Linear/Notion) cannot be overridden for the generic API; authored wrappers keep their login flow.

Settings writes use atomic temp-file rename with mode 0600.

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Note

Add kernel-owned generic MCP runtime with HTTP and stdio transport support

• Adds rlm/mcp.py, a new kernel-owned MCP client registry supporting HTTP (with OAuth/bearer auth) and stdio transports, with tool discovery, invocation, lifecycle management (reload/close), and automatic Jupyter kernel shutdown integration.
• Adds prime-agent mcp add/list/get/remove CLI subcommands backed by mcp-command.ts and routed through public-command.ts; /mcp in the TUI gains the same subcommands.
• Exposes mcp.list_tools and mcp.call_tool as pre-imported Python APIs in the kernel bootstrap; the system prompt advertises enabled generic MCP servers with usage examples when IPython is active.
• Introduces SettingsManager.getGlobalMcpServers/setGlobalMcpServer/removeGlobalMcpServer for managing MCP server configs scoped to global (user-level) settings only, replacing the previous merged-settings approach.
• Settings writes are now atomic (write-then-rename, mode 0600) in settings-manager.ts.
• Diagnostic output from stdio server stderr is captured, bounded, and redacted of secrets before surfacing in McpStartupError.
• Risk: McpServerConfig shape changed (env values are now {"env": "NAME"} tag objects for stdio; getMcpServers() replaced by getGlobalMcpServers()), which may break existing integrations relying on the prior merged config behavior.

^{Macroscope summarized ce6c27b.}

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