Implement shared "applyRefactorings'" function

[rwe]

The original limited applyRefactorings is still exposed, but the logic of both that and runPipe is now shared by a single function, which allows API users to set additional options such as language settings or implement custom hint application loops.

Done in response to #41 and motivated by the new functionality exposed in #44.

This PR includes #45 (Fail with error on unrecognized language pragmas), since this moves that function and otherwise would require some manual merge resolution. But otherwise doesn't depend on it.