(cons '("\\.md" . markdown-mode) auto-mode-alist))
That \\.md should be \\.md\\' otherwise it'll match every filename containing the sequence .md anywhere. (I.e. You already weren't limiting your usage to just matching filename extensions. For instance /home/alper/.mdir/foo/bar.c would match your pattern.)
As you can see, the ...
Since I don't want to accidentally loose any edits in buffers I have open, I have a key bound to revert all buffers, I just run this command when making large changes to the repository which Emacs's wont be tracking.