Some modules can be auto-updated in backoffice by clicking the update button. However if the module is from an other source than prestashop itself (e.g. github) the module needs - afaik - to be updated manually.
So how should one handle updates?
Download ZIP and
unzipit over the corresponding modules folder (/modules/acme/)- unzip and
rsyncit to/modules/acme(rsync -trv /tmp/acme /modules) - Same as 2 but with
--delete - Delete the folder completely and unzip the new one in place like
rm -rf /modules/acmeandcp -a /tmp/acme /modules/acme - Others ...
Side note: what about the config.xml and possibly other generated files?
Same applies for theme updates, how to handle these?
Concerning current version Prestashop 1.7+.