One can use git pull with addons *only if* ... *only if* ... the addon code was acquired via git repos for those addons. Look for a hidden .git directory in those plugin directories. If not there, plugin was not installed using git.
Other wise a git pull at code root of the moodle acquires *only* ... *only* ... core code.
To update the plugins either use Admin GUI interface for upgrading plugins via Moodle plugins server or manually acquire the zip files for the plugins and upgrade manually.
See: https://docs.moodle.org/311/en/Installing_plugins
'SoS', Ken