Simply put, a "shoo fly" track is a temporary track constructed to rearrange train traffic for some temporary condition - usually construction. In this case, it is simply to move the mainline Framingham-Worcester track away from the Boston Landing station construction.
The details after the read more...
Based on a number of reports, I'm very confident that the new Boston Landing station will be a 'center platform' station. This means that one platform will serve both tracks - the platform will be between the tracks and the doors of both inbound and outbound coaches will open onto the platform across from each other.
Knowing that, here is a diagram of what I think the final track configuration might look like. Note that this is my guess. It is possible that CP 4 will be eliminated or replaced with only a crossover from eastbound track 1 to eastbound track 2, since both those crossover switches are not necessarily needed. And the freight lead into Beacon Park could be at CP 4 or east of the new Boston Landing station. But this gives you a general idea of what they're building.
Boston Landing station is scheduled to open in the Fall of 2016. There have been reports that it will initially have only 2 trains stopping during both the AM and PM rush hours, but as we know, schedules are a hot topic right now, so we'll see. Visit the Boston Landing station wikipedia page for more information.