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Strong -1 without a functional replacement that provides comparable LD_PRELOAD capabilities (it also needs a full PEP that analyses all of the ways that setuptools and other packaging utilities use these files, such as for the implementation of "develop" mode, and the processing of ".lnk" mode).
This change also needs to account for the Windows-only "._pth" files that override the path completely.
The main discussion list for such a PEP should be distutils-sig, *not* python-ideas or import-sig (since distutils-sig is where we're more likely to find folks that are actually relying on the feature, and hence have a clearer idea of what will need to change to maintain a comparable level of ecosystem level capability).
https://bugs.python.org/issue14803 is also related, as pth file processing should at least be delayed to run later than it does currently, and because "run code at startup" is one of the capabilities that would need replacing.