Dynamic or managed languages can often ignore most of the hassle with system packages.
You're misinterpreting that guideline. The text says (my emphasis):
> Most programming languages offer a packaging system for distributing support libraries, such as CPAN for Perl or Rubygems for Ruby. Libraries installed through a packaging system can be installed system-wide (known as “site packages”)
It's not saying not to depend on the operating system (of which glibc is part), it's saying not to require particular language package manager packages to be installed on the machine.
Agreed that the other ones you mention are silly, though. Especially the one about environment variables - that isn't actually reasoned advice, it was just the authors writing down what was most common in Ruby development at the time, on the assumption that that must be the best thing to do.
Personally, i would pick a config file over environment variables any day: easier to manually inspect and tweak, easier to give structure to, doesn't get implicitly passed down to subprocesses, can be secured with familiar file permissions, etc.
Environment variables exist on just about EVERY runtime, changed without requiring a pipeline run.
However, subprocess is interesting but I've never run into subprocess that is not sharing a config. Where I worked, if you have subprocess that can't see those configs, you create a new service.
If your point is that existing managers support setting environment variables but not creating config files, then sure. But that isn't a fundamental truth, it's just working with the tools you have.
It just seems far easier to have your kube config inject the env variables from your kube file and that way you don't have to worry during deployment how to add that file and you don't check it into the source. This applies to basically any way you deploy your app, especially containerised ones. Unless you're running your app in an EC2 machine where you can go in and easily edit the file (not that you can't do it in a container), it just seems like extra steps. I've found the happy medium to be sourcing default configs from a file that can all be overridden through env variables
But there's no fundamental reason for that to be the case. You could imagine a very nearby parallel universe where Kubernetes config files don't let you set environment variables, but do let you inject files. In this universe, you can see other deployment approaches that make config files easier (Puppet and suchlike). And if you're building something from scratch, you can make the choice.
Nevertheless, glibc is not the only system dependency which is often used by apps, another such example is JVM of a specific version, which is not tracked by any of the popular JVM build tools and package managers; and OpenSSL, which is too installed by the system package manager.
Dockerfiles exists to fix this by defining all the necessary installation steps as a sequence of instructions, but this is far from a proper package manager.
And not just libc - on a typical unix, there are a small number of other libraries which constitute part of the operating system, like libm, libdl, and libpthread. They are part of the means by which the operating system delivers the POSIX environment.
You're right that the JVM is a dependency, and that there is very poor versioning support for it in production. Everywhere i've worked, we've come up with ad-hoc solutions for it, and none of them have been very good.
Where did you see that being expressed?
They do mean that a repo = a codebase. A remark about "set of repos" is just a technicality of distributed VCSs, meaning that each copy cloned from a single source (or from other copies) is a single repo.
There is a U-shaped utility to monorepos. Most projects fall in the middle somewhere, largely ones managed by independent engineering teams that have no centralized platform/devops/whatever-we-are-calling-it-these-days team.
We disagree on fundamentals then and I think more of the world agrees with me and with the 12 factors.
If they're deployed separately, they don't share the release cycle. Sooner or later you'll end up with mismatched versions of them running (e.g. perhaps one piece fails to deploy). So you need to be prepared for that, so you want them in separate repos so you can easily test with different versions.
> This is incredibly hard to achieve in practice if you're not running something nix, and even then there are leaks of dependencies on kernel syscall APIs. Every Rust app implicitly depends on a glibc (except musl ones), which is present in major Linux distros except slim ones such as Alpine.
Most higher-level languages avoid depending on a specific glibc; as long as you have a working runtime for that language then your app will work with it. And sure in some cases you resort to docker or something. It can indeed be hard but that doesn't mean it's not worth doing.
In that case I'll just rollback the first one. I see no reason to logically decouple two processes into two services when the separation is technically driven. They share the queues, the database, the domain, further division will just make things more complex with no obvious advantage.
At that point you're not deploying separately any more. They explicitly say you can have multiple processes and process types as part of the same app (see #8). The point is that "repo of its own" should align with "atomic unit of release/deployment".
1. One app - one repo. There is nothing fundamentally wrong with multiple apps (as in separate pods/containers/processes) being developed in a single repo, as long as they are tightly coupled functionally, share the release cycle, but still need to be deployed separately to get advantages of separate processes and independent scaling. The first example that comes to mind is separation of public api and worker processes, e.g. ruby's sidekiq, python's celery or a generic kafka consumer.
2. > A twelve-factor app never relies on implicit existence of system-wide packages.
This is incredibly hard to achieve in practice if you're not running something nix, and even then there are leaks of dependencies on kernel syscall APIs. Every Rust app implicitly depends on a glibc (except musl ones), which is present in major Linux distros except slim ones such as Alpine. In fact, the whole Docker crutch IMO is needed specifically to alleviate this problem.
3. > The twelve-factor app stores config in environment variables
It seems to me much more brittle, as it forces you to store secrets in envs, which could be less secure, and to abandon structured file configs, which may enjoy type safety, IDE autocomplete and automatic parsing. With envs you are forced to implement parses for non-trivial and non-string config vars yourself. In fact, envs are often committed into repos as well in form of dot-env files, so the point about commit-safety is moot as well.