For schema/index changes I prefer migrations. These should be committed along side the code, tested, and promoted through environments. This largely prevents dependency issues because the migrations are ordered.

Devops is like 80% dependency management. It's painful initially but you have to crack down on manual changes to production - all production changes should be defined in code, committed to git, tested, and flow through non-prod environments first. (just had an outage yesterday that was essentially because I failed to do this)