Also the Pixi intro module has been split into intro/main modules, so it's intro/outro modules can be excluded cleanly without being tied to the body of the Pixi code. Finally the Pixi into/outro exclusion is tied to Phaser's excludes, ie if Phasers intro/outro is excluded so are Pixi's - this could be separated by giving pixi it's own module list but I can't see why anyone would not want to exclude the wrappers from both, they can always generate the Phaser/Pixi modules in separate passes if they want differing wrapping anyway.
Ninja Physics is no longer included in the build files by default. Not enough people were using it, and not enough contributions were coming in to help polish it up, so we've saved the space and removed it. It's still available in the grunt build files if you require it, but we're deprecating it from the core library at this time. It will make a return in Phaser3 when we move to a modular class system.