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

docs/emacs/packages/exwm.org

@@ -224,7 +224,7 @@ mode), except for ~s-RET~ which opens an eshell terminal.
 #+end_src
 
 A couple of commands are also automatically executed through my
-~autostart~ script written [[file:bin.org::#Autostart-a99e99e7][here]].
+~autostart~ script written [[file:/scripts.md#autostart][here]].
 #+name: exwm-autostart
 #+begin_src emacs-lisp :tangle no
 (exwm/run-in-background "autostart")

docs/emacs/packages/programming.org

@@ -746,7 +746,7 @@ installed this major mode.
 #+end_src
 
 *** Shells
-Aside from Eshell, my main shell on my machine is fish (see my [[file:fish.org][fish
+Aside from Eshell, my main shell on my machine is fish (see my [[file:/fish.md][fish
 config]]), therefore I need a mode for it.
 #+begin_src emacs-lisp
 (use-package fish-mode
@@ -900,7 +900,7 @@ when entering ~lisp-mode~.
 #+end_src
 
 Sly enables some deep interactivity between Emacs and a CommonLisp
-application running the Slynk backend. For an example, see [[file:stumpwm.org::#Utilities-Sly-kkok6oi0yaj0][my Sly
+application running the Slynk backend. For an example, see [[file:/stumpwm/utilities.md#sly][my Sly
 configuration for StumpWM]].
 #+begin_src emacs-lisp
 (use-package sly