Choosing Writing Samples for Ph.D application The following is the description for the required writing samples:

"You must submit at least three papers that best represent your ability to conduct research and write effectively about your area of specialization. We encourage you to submit published work."

I view "three papers" as three different articles (rather than three publications such as conference papers) and, say, could make choices from the below options: 

a. A conference paper on which I am the first author (4 authors in total)

b. A conference paper on which I am the second author (3 authors in total)

c. My Master's thesis which is extended from a. (pretty much the same with a. in the abstract section)

d. Final project report in the class taken during my Master.

What I am wondering is that if I can just combine all four without modification in a single pdf file (about 60 pages total), or I am supposed to extract the main idea in the articles and make it as short as possible.

Another thing is that since c. is just the extension of a., so their abstract sections are pretty much the same. Is it redundant to include both of them?
I'd suggest not to submit a whole thesis. Imagine the frantic look the admission committee members would have when they found out they just printed hundreds of pages.

Ultimately, they care if you can publish. So, definitely keep a and b, and focus on them heavily. For c, I'd suggest do a bit of curating and pick the most interesting chapter that does not overlap with a and b in contents. If none, then I'd suggest the literature review chapter. It's a good section to show your understanding of the field and your skill of information synthesis. 

As for d, they only ask for three; course work (in my opinion) is not worth breaking the quota for. I'd, however, consider submitting if i) it features an extremely innovative idea which may become one of your study objectives, or ii) it acts as the foundation of your then Master's work and publication. It would show that you have the ability to carry and idea forward to fruition, and that's always a plus.

Good luck with the application!