Change the `notifyRootUpdated` API to be transaction based.

This means that in-place, or root, updates need to use explicit calls to `startRootUpdate`, `finalizeRootUpdate`, and `cancelRootUpdate`. The major benefit of this change is that it enables in-place updates in DialectConversion, which simplifies the FuncOp pattern for example. The major downside to this is that the cases that *may* modify an operation in-place will need an explicit cancel on the failure branches(assuming that they started an update before attempting the transformation).

PiperOrigin-RevId: 286933674