Avoid symlinking the contents of /usr into PyPy3 virtualenvs

PyPy >= 3.8 supports a standard prefix installation, where older
versions always used a portable/developent style installation.
If this is a standard prefix installation, skip the logic that symlinks
libraries in a portable PyPy distribution.

Fixes: #2309

docs/changelog/2310.bugfix.rst

@@ -0,0 +1 @@
+Avoid symlinking the contents of ``/usr`` into PyPy3.8+ virtualenvs - by :user:`stefanor`.

src/virtualenv/create/via_global_ref/builtin/pypy/pypy3.py

@@ -42,6 +42,11 @@ def to_lib(self, src):
     def sources(cls, interpreter):
         for src in super(PyPy3Posix, cls).sources(interpreter):
             yield src
+        # PyPy >= 3.8 supports a standard prefix installation, where older
+        # versions always used a portable/developent style installation.
+        # If this is a standard prefix installation, skip the below:
+        if interpreter.system_prefix == "/usr":
+            return
         # Also copy/symlink anything under prefix/lib, which, for "portable"
         # PyPy builds, includes the tk,tcl runtime and a number of shared
         # objects. In distro-specific builds or on conda this should be empty