Does a refactoring (able do conscious language-aware rename classes/variables renaming and replace simple constructions instead of doing dumb string search-and-replace) tool exist which can be used without IDE/editor?
I am particularly interested in Scala, C# and PHP languages.
Not exactly what you are looking for, but Bicycle Repair Man, a Python refactoring tool, ships as an editor-agnostic refactoring library. It's actually used via editor/IDE plugins though.
For Scala there is a refactoring library that can be used standalone: http://scala-refactoring.org/