Upgrade mcp dependency from 1.x to 2.0

[Copilot]

mcp 2.0 changes the low-level Server API: the @server.list_tools() / @server.call_tool() decorators are replaced by on_list_tools / on_call_tool constructor kwargs, handlers take (ctx, params) instead of (tool_name, arguments), and server.request_handlers[...] and response .root unwrapping are removed. In dsagt only the dispatch shell and the test harness touch the SDK Server object; the four *_tools.py concern modules build types.Tool(...) and return plain str/dict, which is a dsagt-internal contract and is unchanged.

Fixes #39.

Dependency
pyproject.toml: mcp>=1.0.0,<2.0.0 → mcp>=2.0.0,<3.0.0. The upper bound is pinned because the SDK has now shipped two breaking majors. The lockfile resolves to mcp 2.1.1; all verification below ran against that version.

Dispatch shell (src/dsagt/mcp/server.py)
build_dispatch_server():

Passes on_list_tools / on_call_tool callables to Server(...) instead of using the removed decorators.
on_list_tools returns types.ListToolsResult(tools=...) instead of a bare list.
on_call_tool(ctx, params) reads params.name / params.arguments and returns types.CallToolResult(content=[...]) instead of a bare content list.
on_call_tool rejects a missing or non-dict params.arguments with a ValueError rather than defaulting silently.
Per-tool dispatch (span opening, ValueError → error dict, str-vs-dict formatting) is unchanged.

async def on_call_tool(ctx, params: types.CallToolRequestParams) -> types.CallToolResult:
tool_name = params.name
arguments = params.arguments
handler = handlers[tool_name]
...
return types.CallToolResult(content=[types.TextContent(type="text", text=text)])

return Server(name, on_list_tools=on_list_tools, on_call_tool=on_call_tool)
_run_stdio, create_dsagt_server, and main() are untouched: mcp.server.stdio.stdio_server, NotificationOptions, InitializationOptions, and server.get_capabilities(...) are stable across the bump.

Test harness
tests/mcp_helpers.py (call_tool_sync / call_tool_async) uses server.get_request_handler("tools/call" | "tools/list").handler in place of the removed server.request_handlers[...] dict, and drops the .root unwrap.
The inline copies of that helper in test_dsagt_server.py, test_kb_search_filters.py, test_knowledge_server.py, and test_memory_tools.py are replaced by the shared mcp_helpers.py versions.
tool.inputSchema reads in tests are changed to tool.input_schema; mcp 2.0 renamed the Python attribute on types.Tool. The inputSchema= constructor kwarg still works through the pydantic alias, so production tool-building code is unaffected.
The subprocess-based helpers (mcp_call_tool, mcp_initialize) exercise the wire protocol and needed no change.
Verification
Rebased onto main after #41 (Template compliance); no conflicts. uv sync --all-groups after the rebase produced no lock change.

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 tests/test_server_startup.py -q

121 passed

uv run ruff check src/dsagt/mcp tests/mcp_helpers.py tests/test_dsagt_server.py
tests/test_kb_search_filters.py tests/test_knowledge_server.py tests/test_memory_tools.py

All checks passed

uv run black --check

6 files would be left unchanged

test_server_startup.py starts the real server over stdio and is the direct check for the 'Server' object has no attribute 'list_tools' failure reported in #39 with a fresh mcp 2.x install.

• Fixes Upgrade mcp dependency from 1.x to 2.0 #39

[github-actions]

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[jeanbez]

While testing, I saw these two:

1. Previously @server.call_tool() validated against inputSchema by default, which does not seem to be the case now, so every malformed agent call now reaches the handler raw. This should resolve that:

    jsonschema.validate(instance=arguments, schema=schemas[tool_name])
except jsonschema.ValidationError as e:
    result = {"status": "error", "error": f"Input validation error: {e.message}"}

Plus this in server.py line 92 (after tool_category):

schemas = {tool.name: tool.input_schema for tool in tools}

2. arguments can be None. The PR does arguments = params.arguments adding or {} should resolve the issue

arguments = params.arguments or {}

Together they turn a clean Input validation error: 'query' is a required property into Unexpected error: 'NoneType' object is not subscriptable, plus a full traceback in the server log for what is a client-side error.

[shreddd]

@jeanbez - we don't strictly need to accept this PR either. Let's discuss more today.

[aarontuor]

Straightforward changes updating to mcp >2.0. Tested and no regressions or side effects but was able to recreate the fault Jean Luca described. Was able to recreate Jean Luca's bug though.

Was able to recreate Jean Luca's bug.