IDE's are good at treating the symptoms. But it's also possible to write the code so that you don't need an IDE to untangle it: For example keeping all variables within (file) scope, and abstracting out into reusable (reusable elsewhere) libraries.
You can make functions pure and specific so they rarely need to change. And use name-spaces and naming conventions - so the variables can be found with grep (find in files).
Lets say you are upgrading an API, lets call it "HN", to a new major version, which has made a breaking change by renaming HN.foo to HN.bar. Now if you have always named the API "HN" you can just make a "replace in file" operation where you replace HN.foo with HN.bar - after you have already checked that there is no HN.foobar (to prevent HN.barbar)
Even sophisticated IDE's will have trouble following functions in a dynamic language that is passed around, renamed, returned, etc. So I would never trust an IDE to find all calls-sites.
Heavily depending on an IDE or tooling can also lead to over-use of patterns and boilerplate that the IDE handles well. And unnecessary work like adding annotations just to satisfy the tooling.
Not GP, but for most programs I write myself I cannot find all the call sites of a certain function because of using first class functions a bunch. When I worked in nginx I had a smaller amount of similar trouble, since nginx frequently but not pervasively uses function pointers to decide what to do next.
