I am experiencing the same issue, and yes, reverting does bring back the default context options. This led me to believe the issue was related to a package so after a revert I installed ONLY will bonds package control (using these instructions: http://wbond.net/sublime_packages/package_control/installation#ST3) and then installed the SideBarEnhancements package.
Result: in St2 context options are there, in st3 most are not.
Note: ST3 is still in beta; package control for ST3 is still in alpha. This post is not a complaint, just a bug report.
Keep up the great work