Add MCP (Model Context Protocol) server support as an integration

[mattprintz]

Summary

Adds Model Context Protocol servers as a first-class Beaker integration type,
alongside supporting refactors to the integration-provider framework that MCP
builds on. Users can discover, add, edit, and use MCP servers (stdio or
HTTP/SSE) from the Integrations UI; the agent can list and call their tools,
read their resources, and use their prompts.

What's included

MCP integration provider (backend)

• New MCPIntegrationProvider (lib/integrations/mcp.py): discovers servers
  from mcp.json / .mcp.yaml config files (conventional mcpServers /
  servers layout) across project, user, and context search roots.
• Kept-open sessions via a per-server owner task. Each server's
  ClientSession lifecycle (connect, every request, disconnect) is confined to
  one dedicated asyncio task (_ServerConnection). Callers on any task submit
  closures over an asyncio.Queue and await per-request futures; requests are
  serialized. This resolves the anyio "cancel scope in a different task" error
  from opening a session on one task and tearing it down on another, and avoids
  paying subprocess-startup cost on every call.
• Fail-early startup. Connect + initialize() are isolated so a failed
  handshake surfaces the real exception cleanly (rather than being masked by
  anyio task-group teardown) and never leaves a hung owner task. stdio stderr
  is captured and attached to the error to aid debugging.
• Tools/resources/prompts exposed as typed resources (MCPToolResource /
  MCPResourceResource / MCPPromptResource); the agent gets generic dispatch
  tools (connect_to_mcp_server, list_mcp_tools, call_mcp_tool,
  read_mcp_resource).
• Mutation: add / update a locally-configured server, written back to a
  user-writable config (~/.beaker/mcp.json by default, or an existing
  writable config the provider already reads).

Integrations UI (frontend)

• MCPIntegrationViewer (read-only), MCPIntegrationEditor (full add/edit
  form: transport, command/args/env or URL/headers, display name, description),
  and MCPToolsPanel (read-only tool catalog with argument schemas).
• Context-provided servers (namespaced under a context-<slug> corpus) are
  read-only ("View"); locally-configured servers are editable ("Edit").
• "New Integration" is now a split button offering "Specialist Agent" (adhoc)
  and "MCP Server".
• Instructions are shown read-only (reported by the server on connect; not
  persisted to config).

Integration framework refactors (enabling MCP, shared with skills)

• BaseIntegrationProvider: dropped the display_name constructor arg (now a
  class attribute), added an async cleanup() hook, a from_context() hook,
  and an optional icon classvar. Documented the one-instance-per-class /
  merge fold invariant.
• IntegrationProviderRegistry: documented the folding invariant;
  system_preamble now renders as per-provider markdown sections.
• SkillIntegrationProvider: discovery refactored to share a
  discover_integration_paths / from_context structure with MCP; prompt
  output moved to YAML. Context skills now load via from_context rather than
  bespoke logic in BeakerContext.
• BeakerContext: DEFAULT_INTEGRATION_PROVIDER_CLASSES (skills + MCP);
  split default_integration_providers / context_integration_providers;
  cleanup() is now async and gathers subkernel + integration cleanups.
• BeakerSubkernel.cleanup() is now async; subkernel system-preamble rendered
  as YAML.
• Kernel shutdown path made async end-to-end; the shutdown handler stops the
  loop via call_soon(loop.stop) after cleanup completes.

Other

• call_in_context REST bridge returns structured {status, ename, evalue}
  error payloads; integration-id route regex accepts : (for
  mcp:<corpus>:<name> uuids).
• handle_message.__aexit__ matches on exc_value (instance) rather than
  exc_type (class) — the CancelledError branch never fired before.
• Added mcp and pyyaml dependencies; .gitignore for personal .mcp.* /
  .skills.json config.

Testing

• New tests/integrations/mcp/test_mcp_provider.py (73 tests): pure helpers,
  config parsing/discovery, the _ServerConnection actor lifecycle (reuse,
  disconnect, startup failure, init error, run-after-close), catalog
  population, prompt rendering, and dispatch tools. No live servers contacted.
• Full suite green (452 passed).