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You open up the code, find all of the secrets (e.g. using high-entropy substring search), replace them with access to a global variable, and set it from a file set by a configuration from a command line.Huh? Amazingly you make it sound so easy when it's anything but. Where is this file? How is it deployed? How is it rotated? If I have 10,000 VMs, how do I deliver that file to those machines? If my VMs aren't persistent, how do I ensure new VMs are deployed with this file?
Or were you thinking that they would just ssh into production and scp the file into there? To me you glossed over so many details that you hardly solved the problem at all. Replacing the secrets in source code is the _easy_ part. Deploying secrets is the hard part.
There are tools out there to make this easy, but (1) they almost always make things harder for developers and (2) they almost always require a large infrastructure change. Sure, if your deployment is small enough where you could just SSH into a single prod server and scp a file - then you are likely miles ahead - in terms of both security and culture, but changing the culture is harder than it looks.
I don't want to sound like I am making excuses for them - but I only want to show how shortcuts when you are small can snowball into a culture where you have a gaping wound that may be difficult to fix.