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g-i includes an old version of pep8 and pyflakes and uses that
during "make check".
It (1) doesn't catch all cases newer versions of pycodestyle/pyflakes catch
and (2) doesn't test all Python files (3) doesn't work with meson.
Instead of updating just remove them and depend on flake8 instead.
To run the checks simply run flake8 in the root dir.
This also makes it possible to run those checks when using meson and
not autotools.
To not get test suite failures on flake8 updates move the checks from
"make check" to an extra "make check.quality" target.
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