fix: make dory mcp serve work on macOS and MCP clients

[yb-sid]

On macOS, launching the MCP Python server with i.e dory mcp serve, runs python3 /dev/fd/3 … 3<<'PY' which executes an empty script under Apple Python, so dory mcp serve exits with no output.

Write the server to a temporary file before running it so stdin stays free for stdio MCP. Rename tool identifiers from dotted names (dory.engine_status) to underscore names (dory_engine_status) so hosts that only accept [a-zA-Z0-9_-] do not drop every tool.

how I tested

printf '%s\n' '{"jsonrpc":"2.0","id":1,"method":"ping"}' \
  | ./scripts/dory mcp serve
# -> {"id":1,"jsonrpc":"2.0","result":{}}

printf '%s\n' \
  '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2025-06-18","capabilities":{},"clientInfo":{"name":"t","version":"0"}}}' \
  '{"jsonrpc":"2.0","id":2,"method":"tools/list"}' \
  | ./scripts/dory mcp serve
# -> 15 tools, all dory_* names