But in the case of say javascript the code is brought together when you run/open the site. Thus you can read it. Or easier is to request the file and its there to read.
You are correct that the vaults cannot read it or know what file the parts are from, but the file has to be readable in order to be loaded into the web page.
The same is not true for compiled programs since the source code is not included. Only if the program is “open sourced” (or similar) would the source code normally be available.