The script pluginGallery.php looks at the Plugin Gallery for your version of OJS, and lists the latest version of each plugin marked as compatible with that version.
The first bash script under " Install the latest version of all missing plugins" selects only those plugins marked with the status of “noInstalledVersion” (not installed) and then:
- clears the existing plugin folder (if any)
- downloads the latest version to /tmp
- extracts the download from /tmp to the plugin folder
- runs the plugin installation script
Similarly, the bash script for “upgrade all plugins” selects only those plugins marked with the status of “installedVersionOlder” (update is available) and then:
- clears the existing plugin folder
- downloads the latest version to /tmp
- extracts the download from /tmp to the plugin folder
- runs the software upgrade script
In my testing, I found that some of the permissions in the tar files weren’t suitable for my hosting default (dedicated apache user with mod_php under RHEL, where apache cannot write to the php files). Specifically, the tar files were packaged with permissions for the user, but not for the group or world. As a result, when I untar’d the plugin as myself, and then ran the install/upgrade as apache, the apache user could not read the new plugin files. I had to change the permissions to allow apache to read the plugin files.
This may be the case with your missed plugins, but will depend on numerous factors specific to your server environment.