Is there a simple way to reinstall all packages that my app depends on (i.e. they are in my apps node_modules folder)?
You can use the reinstall module found in npm.
After installing it, you can use the following command:
reinstall
The only difference with manually removing node_modules folder and making npm install is that this command automatically clear npm's cache. So, you can get three steps in one command.
upd: npx reinstall is a way to run this command without globally installing package (only for npm5+)