Bug Description

MCP/Pydantic tool schemas that encode optional parameters as nullable unions can be rejected by some provider adapters, most visibly Anthropic, before the model can run any tool call.

Example shape emitted by MCP/Pydantic:

{
  "type": "object",
  "properties": {
    "workdir": {
      "anyOf": [{"type": "string"}, {"type": "null"}],
      "default": null,
      "description": "Optional working directory"
    }
  }
}

Anthropic tool input schemas should not receive the null branch. Optionality is already represented by the parent object's required list, so Hermes should normalize the schema to:

{
  "type": "object",
  "properties": {
    "workdir": {
      "type": "string",
      "default": null,
      "description": "Optional working directory"
    }
  }
}

During the same investigation, MCP tools/list_changed notifications can also race with active stdio JSON-RPC requests. The notification handler currently refreshes tools synchronously, which can interleave list_tools with normal call_tool/resource/prompt RPCs on the same stdio session and leave user-visible tool calls timing out.

Expected Behavior

• Hermes accepts MCP/Pydantic optional nullable schemas and converts them into provider-safe tool schemas.
• Optional fields remain optional via the parent required array.
• MCP list refreshes should not wedge the session or transiently unregister tools while an agent turn is using them.

Actual Behavior

• Nullable anyOf / oneOf branches can be forwarded into Anthropic input_schema.
• Anthropic rejects the tool schema before the agent can execute tools.
• Dynamic MCP tools/list_changed refreshes can run concurrently with user-triggered stdio RPCs, causing timeouts/stale tool races.

Reproduction Notes

1. Register/use an MCP server whose tool input schema includes optional fields represented as anyOf: [{...}, {"type": "null"}] or oneOf: [{...}, {"type": "null"}].
2. Use an Anthropic-backed model/tool adapter.
3. Trigger a turn where Hermes sends that tool schema to the provider.
4. Provider validation fails before tool execution.

For the stdio race, use an MCP server that emits tools/list_changed shortly after initialize while the agent is starting or calling another MCP tool. mongodb-mcp-server is one observed example.

Proposed Fix

• Normalize MCP input schemas by collapsing nullable anyOf/oneOf unions to the single non-null branch, preserving metadata (title, description, default, examples).
• Apply the same normalization in the Anthropic adapter as a final provider-side guard.
• Serialize client-initiated MCP RPCs per server with a lock.
• Handle tools/list_changed refresh asynchronously and avoid deregistering tools before re-registering replacements, reducing stale-handler windows.

Validation

A local patch adds/updates tests covering:

• nullable optional field collapse in MCP schema normalization
• nested nullable array item collapse
• Anthropic tool conversion stripping nullable unions
• existing MCP schema shape repair behavior

Local commands run:

python -m pytest tests/agent/test_anthropic_adapter.py::TestConvertTools tests/tools/test_mcp_tool.py::TestSchemaConversion -o 'addopts=' -q
# 20 passed

python -m py_compile agent/anthropic_adapter.py tools/mcp_tool.py tests/agent/test_anthropic_adapter.py tests/tools/test_mcp_tool.py
# passed