fix: restore broken links

docs/emacs/packages/applications.org

@@ -498,7 +498,7 @@ configuration for the ~mu4e~ package itself.
 Quick sidenote: on Arch Linux, you’ll need to install either ~mu~ or
 ~mu-git~ from the AUR in order to use mu4e. I also have a ~.desktop~ file
 to make it possible to open mu4e directly from my program picker. It
-uses the shell script ~emacsmail~ I’ve written [[file:bin.org::#Emacsmail-afffb7cd][here]].
+uses the shell script ~emacsmail~ I’ve written [[file:./scripts.md#emacsmail][here]].
 #+header: :mkdirp yes
 #+begin_src conf-desktop :tangle ~/.local/share/applications/mu4e.desktop
 [Desktop Entry]
@@ -1092,7 +1092,7 @@ notification system, and I’ll activate the modeline notification.
 EMMS, also known as the /Emacs MultiMedia System/, allows the user to
 interact through Emacs with multimedia elements such as music and
 videos. My main use for it will be for music with MPD (see its
-configuration [[file:mpd.org][here]]).
+configuration [[file:/mpd.md][here]]).
 #+begin_src emacs-lisp
 (use-package emms
   :defer t