I think this is a weird problem that happens when you put two ionic project in the same place (under the same directory) let's say:
-- workspace
|-- moodlemobile
|-- anotherionicproject
It happened with me at the beginning when I started working on a custom moodle app, where I put the official mobile app and my custom app under the same directory and I started working, when I install the plugins and platform for the second (custom app) they will be installed out of the app folder, perhaps you can check if the plugins and platforms folder exist in your project or outside of it.
the solution is to put them in separate directories ( I mean parent directories) like:
|__workspace
|__ moodle
| |__ moodlemobile
|__ Others
| |__ anotherionicproject
Hope this will solve your project.