Transportation officials inked a new 10-year deal with the Greenway Conservancy this week, even after the state’s top fiscal watchdog urged them to hold off while his probe of the nonprofit’s spending is under way.The revelations — detailed in a letter Inspector General Glenn Cunha sent to MassDOT officials weeks ago — add an immediate layer of scrutiny to the newly hatched deal with the Greenway, which relies on a combined $14 million in state, city and private funds to keep the 17-acre park operating.