Why did you intentionally change the original semantics of g:ghcmod_use_basedir? Currently it holds a path, but you're changing it to a flag.
I think it is enough that s:system() defaults to be run in ghcmod#basedir().

For configuration file backward compatibility. So, I can remove this parameter at all.

For users who define g:ghcmod_use_basedir, your change breaks compatibility because the meaning completely changes. For users who doesn't, the compatibility is kept. Right?

I think it is better to keep the compatibility for g:ghcmod_use_basedir users. Also, the current g:ghcmod_use_basedir is more general because it can simulate the current default behavior by :let g:ghcmod_use_basedir = expand('%:p:h').
My suggestion is like this.

diff --git a/autoload/ghcmod.vim b/autoload/ghcmod.vim
index 08bb3c1..60f1ffc 100644
--- a/autoload/ghcmod.vim
+++ b/autoload/ghcmod.vim
@@ -457,10 +457,10 @@ endfunction"}}}

 function! ghcmod#basedir()"{{{
   let l:use_basedir = get(g:, 'ghcmod_use_basedir', '')
-  if !empty(l:use_basedir) && l:use_basedir ==? 'yes'
+  if empty(l:use_basedir)
     return s:find_basedir()
   else
-    return expand('%:p:h')
+    return l:use_basedir
   endif
 endfunction"}}}

You are right. I had made changes two month ago and forgot some details. Sorry.

I agree with you.

Okay. I merge this PR and make such a modification.
Thank you.