Upgrade `mcp` dependency from 1.x to 2.0

[ajtritt]

Summary

Bump the mcp (Model Context Protocol Python SDK) dependency from the current >=1.0.0 (installed: 1.28.0) to mcp>=2.0.0,<3.0.0. This is a major version with breaking API changes, but the blast radius in dsagt is small and fully scoped below.

Background

mcp 2.0.0 reworked the low-level Server API (dsagt uses mcp.server.lowlevel.Server, not FastMCP) to support the 2026-07-28 MCP spec. Verified directly against the installed mcp==2.0.0 package (not from training-data memory, which predates this release):

• @server.list_tools() / @server.call_tool() decorators are removed. Handlers are now passed as on_list_tools= / on_call_tool= kwargs to the Server() constructor.
• on_list_tools(ctx, params) must return types.ListToolsResult(tools=[...]), not a bare list.
• on_call_tool(ctx, params: types.CallToolRequestParams) replaces (tool_name: str, arguments: dict) — read params.name / params.arguments.
• on_call_tool must return types.CallToolResult(content=[...]), not a bare list[TextContent].
• server.request_handlers[SomeRequestClass] (dict keyed by pydantic request classes) is removed. Public replacement: server.get_request_handler("tools/call") / "tools/list" (string-keyed), returning HandlerEntry(params_type, handler).
• Response wrappers no longer have .root (the RootModel union pattern is gone) — read result.content[0].text directly.

Confirmed unaffected by a real import/construction smoke test against mcp==2.0.0: mcp.server.stdio.stdio_server, mcp.server.lowlevel.NotificationOptions, mcp.server.models.InitializationOptions, server.get_capabilities(notification_options=, experimental_capabilities=), and types.Tool(inputSchema=...) construction (camelCase kwargs still populate via pydantic alias).

Practical implication: registry_tools.py, knowledge_tools.py, memory_tools.py, skill_tools.py never touch the SDK Server object directly — they only build types.Tool(...) and return plain str/dict, which is a dsagt-internal contract. Only build_dispatch_server() in src/dsagt/mcp/server.py (~50 lines) talks to the Server class.

Scope

1. pyproject.toml / uv.lock — bump to mcp>=2.0.0,<3.0.0 (pin the upper bound given the demonstrated history of breaking majors), uv sync.

2. src/dsagt/mcp/server.py — build_dispatch_server() — replace the decorator-based list_tools()/call_tool() with on_list_tools/on_call_tool callables passed to Server(name, on_list_tools=..., on_call_tool=...). Preserve the existing per-tool dispatch logic (span opening, ValueError → error-dict, str-vs-dict formatting) as the body of on_call_tool; only the outer signature (ctx, params in; types.CallToolResult out) and on_list_tools (wrap in types.ListToolsResult) change. _run_stdio, create_dsagt_server, and main() are untouched — they only call server.run(...) / server.get_capabilities(...), both stable across the bump.

3. Test harness — 5 files reach into server.request_handlers[...] / .root, which no longer exist:

   • tests/mcp_helpers.py (call_tool_sync / call_tool_async, used broadly)
   • tests/test_dsagt_server.py (_list_tools / _call helpers)
   • tests/test_kb_search_filters.py, tests/test_knowledge_server.py, tests/test_memory_tools.py (inline copies of the same pattern)

   Fix: replace server.request_handlers[types.CallToolRequest] with server.get_request_handler("tools/call").handler (pass ctx=None — dsagt's own handler never touches it), same for "tools/list", and drop the .root unwrap. Verified this pattern end-to-end against real mcp==2.0.0.

   tests/mcp_helpers.py's subprocess-based helpers (mcp_call_tool, mcp_initialize, real JSON-RPC over stdio) are unaffected — they exercise the wire protocol, not SDK internals.

   Open question: the 3 inline copies (test_kb_search_filters.py, test_knowledge_server.py, test_memory_tools.py) duplicate the same helper logic already in mcp_helpers.py. Since all three need to be touched anyway, consider consolidating them onto the shared mcp_helpers.py versions instead of patching each copy in place.

Verification

• uv run black .
• uv run ruff check .
• uv run --no-sync python -m pytest tests/test_dsagt_server.py tests/test_registry_server.py tests/test_knowledge_server.py tests/test_memory_tools.py tests/test_skill_tools.py tests/test_kb_search_filters.py -q
• Skip the network/subprocess integration suites (test_integration.py, test_*_integration.py, test_server_startup.py, test_dependency_integration.py) unless something above regresses them.