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This commit rewrites our ancient `./configure` script from shell into Python.
The impetus for this change is to remove `config.mk` which is just a vestige of
the old makefile build system at this point. Instead all configuration is now
solely done through `config.toml`.
The python script allows us to more flexibly program (aka we can use loops
easily) and create a `config.toml` which is based off `config.toml.example`.
This way we can preserve comments and munge various values as we see fit.
It is intended that the configure script here is a drop-in replacement for the
previous configure script, no functional change is intended. Also note that the
rationale for this is also because our build system requires Python, so having a
python script a bit earlier shouldn't cause too many problems.
Closes #40730
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