Apply-refact shouldn't hardcode `GHC.Paths.libdir` in `parseModuleWithArgs`

[fendor]

From haskell/haskell-language-server#3241, we essentially traced the issue to https://github.com/mpickering/apply-refact/blob/master/src/Refact/Internal.hs#L718.
Our binary distribution uses the wrong libdir because of ghc-paths.

The solution is to allow us to specify the libdir in parseModuleWithArgs, since we do know it.
Additionally, every usage of parseModuleWithArgs needs to propagate this parameter requirement.

[fendor]

In my opinion, we should adapt the API of

applyRefactorings :: Maybe (Int, Int) -> [[Refactoring SrcSpan]] -> FilePath -> [String] -> IO String

to

applyRefactorings :: LibDir -> Maybe (Int, Int) -> [[Refactoring SrcSpan]] -> FilePath -> [String] -> IO String

and let consumers deal with the libdir. They may depend on ghc-paths, but it will be their choice.