Sincesys.prefix is now set to point to the virtual environment before this code runs, addingsys.prefix here is now incorrect, we want to addsys.base_prefix andsys.base_exec_prefix, and because the existing directories inPREFIXES are now already the venv, we want to append the base prefixes instead.

Additionally, resettingPREFIXES whensystem_site isfalse is now unnecessary, because it already has the correct value.

The comment above can also be removed, or moved togetsitepackages, as there's no possibility of us adding a duplicate prefix now.PREFIXES will already have a duplicated prefix from its initialization if we are running on a virtual environment.

Background into this:

GH-126987 moved the venv initialization logic togetpath, the code that initializes the prefixes andsys.path. Previously, that was done here insite, which was somewhat problematic, but you can read about that in the isssue.

So, before that change, whensite, initializedPREFIXES on import, it would effectively be set tosys.base_prefix andsys.base_exec_prefix, which at that point would always have the same value assys.prefix andsys.exec_prefix.¹

Then, here invenv(), if we detect a virtual environment, we would setsys.prefix andsys.exec_prefix tosite_prefix in the snippet above that now issues warnings if we detect a mismatch (link to the change in GH-126987).

- sys.prefix = sys.exec_prefix = site_prefix+ if sys.prefix != site_prefix:+     _warn(f'Unexpected value in sys.prefix, expected {site_prefix}, got {sys.prefix}', RuntimeWarning)+ if sys.exec_prefix != site_prefix:+     _warn(f'Unexpected value in sys.exec_prefix, expected {site_prefix}, got {sys.exec_prefix}', RuntimeWarning)

After that, we either resetPREFIXES to[sys.prefix], ifsystem_site isfalse, or appendsys.prefix, which had now been updated tosite_prefix. We only do this forsys.prefix, and ignoresys.exec_prefix, because in virtual environments there's no distinction, they always have the same value.

Considering thegetpath changes, withPREFIXES getting set to[sys.prefix, sys.exec_prefix] on import, it already includes the virtual environment prefix, so all we need to do here now is to appendsys.base_prefix andsys.base_exec_prefix whensystem_site istrue.