Review README and rearrange to be consistent with what the program does by default

[hlapp]

My recollection is that @megbalk, possibly with some help from @thibaulttabarin, wanted to take care of this. (Unassign yourself if that's not quite right, Meghan.)

[meghalithic]

fix section 2, no. 3) Calculate percentage area of the biggest blob over the total blobs of a particular trait