In my personal projects that use Arduino stuff (or in my case ESP32/8266) I have been using platform.io. In addition to really good IDE integration, it has a way to express library dependencies.
Its way isn’t as fancy as something you’d see with a “real” package manager like NPM but it is good enough that anybody pulling down your source code will know what libraries to install—in fact platform.io will do it for them.
If it was me, I’d switch all the code to use platform.io. It could also help with porting to ESP and teensy as the system helps manage any compiler flags you’d need in order to add platform-specific code.