After upgrading to phpstorm 2016.1, every single time I re-open a project after switching, phpstorm re-indexes the entire project. These are rather large projects and the re-index takes about 2-3 minutes on my i7 vPro / 840 evo ssd laptop, which quickly amounts to half an hour of productivity loss per day on certain days where project switching is frequent. I've got several scripts that interact with my phpstorm window so having multiple projects open at the same time is not a solution I can temporarily impose :(
Build #PS-145.258, built on March 16, 2016
JRE: 1.8.0_76-release-b18 amd64
JVM: OpenJDK 64-Bit Server VM by JetBrains s.r.o
This didn't happen in my previous version, which was 9.