Earlier quoted context omitted.
The initial set of dependencies is being installed via npm, the it installs its own dependencies via ied if told so: https://github.com/alexanderGugel/ied#installation This is a "cool" feature during development, since it's a nice proof of concept. Originally I checked in the node_modules directory, but then reddit was shitting on me as usual (yes, you shouldn't check in node_modules in an actual app, but this is PAC…
Dude, don't listen to reddit when it comes to managing your own open source project.
To the OP: Don't let people bully you. Many people have strong ideas and will want you to do things their way. You aren't going to make everyone happy, though. Somebody will be pissed off no matter what you do (if you are popular enough -- normally people won't pay any attention to you ;-) ). "Because that's what I want to do" is a completely valid reason for any decision on your own project.