Applications Close After Logout

When I log out, all the applications I had open are closed, and they don’t reopen when I log back in. Is there a way to fix this?

There is nothing to fix because nothing is broken, this is normal default behaviour for any serious os.

If you want to have the unusual behaviour of session saved on exit and loaded on login,
try using this incantation:

gsettings set org.mate.session auto-save-session 'true'

or use the GUI app "dconf-editor" to set this value

The alternative is to not logout but just hibernate or suspend

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Instead of log out, you should use the standby feature.

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It can be set in the GUI too via Start-up Applications → Options:

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