The biggest change that I have found is that NEST+M is no longer a "School Based Application School". It has a code number which means that you will rank it on your application, just like you do if you are applying for Mark Twain or PPAS, etc.
There are other City Wide Schools that remain "School Based Application" Schools like ICE and Anderson. It is easy to determine whether you need to rank a school on your application. If it has a code number - you rank it. Whether is screened or lottery or city wide or district wide, if it has a code number, you rank it on the application. In the Directory, if it says, "This school has a school based application process. Contact the school for more information on how to apply." - that is what you do. Charter Schools always remain "School Based Application Schools". You do not rank them and you apply separately to their lotteries (usually from Jan. - late March).
MS 442, The Carroll Gardens School for Innovation, has to move from its PS 32 location in the fall of 2017. There has been speculation about where they might move, but it seems that they may be a little closer to a resolution. There has been a proposal that it move into the Bishop Ford Building in Windsor Terrace. That building currently houses the large Prek Center 280, The Brooklyn Urban Garden Charter School (BUGS), and Stanley Lamm Preschool.
Brooklyn Lab Charter Middle School is opening a second location and will open two new high schools in downtown Brooklyn by 2017.