Much made of the fact that Harbaugh retained Tom Mars as his legal rep for the NCAA violation allegations. Why do that if you were not staying? Also, Sam Webb reports two different dynamics in the negotiations: Agents highlighting the interest from the NFL as a bargaining chip and Santa Ono being a diplomatic and oil-on-the-waters element of negotiations.
I would say that the indications are that Harbaugh wants to stay but needs the wasta of an increase in pay to go forward.