When I attach an external HDD, GNOME suggests opening it with Anjuta:

How can I make it open with Nautilus instead?
Answers:
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Method 1
Most likely it has to do with this commit:
where they changed:
[File Loader] -SupportedMimeTypes=application/x-anjuta-old +SupportedMimeTypes=application/x-anjuta-old,inode/directory
so when installing anjuta, update-desktop-database is run (during post-install); that updates /usr/share/applications/mimeinfo.cache and the default handler for inode/directory becomes anjuta.
To fix this run:
xdg-mime default org.gnome.Nautilus.desktop inode/directory
or manually edit ~/.local/share/applications/mimeapps.list and add inode/directory=org.gnome.Nautilus.desktop under [Default Applications] e.g:
[Default Applications] inode/directory=org.gnome.Nautilus.desktop
or if you already have an entry for inode/directory, make sure org.gnome.Nautilus.desktop is the first in the list.
The command (that you had tried)
xdg-mime default nautilus.desktop inode/directory
no longer works with newer versions of gnome/nautilus because the (gnome) apps are launched using D-BUS activation. As a result, nautilus.desktop no longer exists – it has been replaced by org.gnome.Nautilus.desktop
If editing mimeapps.list has no effect that means your DE isn’t freedesktop.org compliant so maybe it’s time to file a bug report.
All methods was sourced from stackoverflow.com or stackexchange.com, is licensed under cc by-sa 2.5, cc by-sa 3.0 and cc by-sa 4.0