Roof Tarping damage

[Michael Herr]

I just closed on a bank owned foreclosure property.

There is one area where ceiling has caved in a bit and obvious water damage..

Entire roof has been tarped: Seems like its just a flashing issue where valley of roof meets flat roof section.

Entire roof was tarped(even though roof is newer and only needed a small repair): presumably by a guy who was paid by the button cap nail, because there are alot more than needed.

Just blowing off steam, frustrated that the repair to the actual problem was probably cheaper than paying this guy to tarp the whole thing.

Tarp situation probably helped me get the deal so I'll move on to a productive question.

How would you fix this? 

Roofing cement applied over every nail hole?

Replace the shingles?