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Well it was the only place that water could come from, no pipes over there.

ohh, water was coming into the house... that's not a fun situation to deal with...

It looks like there are multiple layers of shingles on the roof. From what I know, after a couple of added layers are placed there, you typically need to scrape everything off and start over new .. hopefully that isn't what you need to deal with --- or maybe you have "homeowner's insurance" that you can use to help offset the costs?