includeJsFile vs includeJsResource
includeJsFile links directly to the file. It doesn't try anything fancy, it just finds the file (exactly as you've referred to it) and creates a normal &lt;script&gt; tag for it.

includeJsResource looks for that file in a few different places. It could be a plugin resource, it could be a native Craft resource, etc.

Whenever possible, stick to includeJsFile.