I'm using the latest xcode (8.2) and everything is ok apart from some specific issues I'm having right now.
A common issue is having a space in the project title which messes up the framework/header/library search paths. Look in build settings > search paths. If the paths have separated into separate lines where your spaces are, edit the paths so that they are each on one line and wrap them in quotes.
Another dirty fix is to change the "$(SRCROOT)/App-Name" path to "recursive" so it looks in all the sub-folders without you needing to specify them all.