Found the problem the command
java -jar /usr/share/jenkins/jenkins-plugin-manager.jar ... (mentioned above) was downloading plugins by default in the same dir as the jar file (/usr/share/jenkins/ref/plugins)
I had to use the option --plugin-download-directory to download it to jenkins’ default plugin directory (or change jenkins’ option --pluginroot)
java -jar /usr/share/jenkins/jenkins-plugin-manager.jar --war /usr/share/java/jenkins.war --plugin-file /usr/share/jenkins/ref/plugins.txt --plugin-download-directory /var/lib/jenkins/plugins/