Hooks
The hooks you’re searching for are
'pre_set_site_transient_update_plugins'
and
'upgrader_post_install'
The later takes three arguments. Example:
function upgrader_post_install_cb( $true, $hook_extra, $result )
and should be used for: Move & activate the plugin, echo the update message.
Moving plugins
Moving works like this:
$wp_filesystem->move(
$result['destination']
,'your_destination_path'
);
Then use activate_plugin( 'path/file' );
after moving.
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