Include all site packages directories in ephemeral environment overlays (#15121)

Related to https://github.com/astral-sh/uv/issues/15113

The case in the linked issue is that we perhaps should not be allowing
`uv run --with` with system interpreters at all. I think we can consider
that, but the issue highlighted that `uv run --with` for a system
interpreter is broken if the base interpreter has custom site packages.
This generalizes beyond system interpreters so we should probably fix
our overlays.

.github/workflows/ci.yml

@@ -1916,7 +1916,7 @@ jobs:
           persist-credentials: false
 
       - name: "Install Python"
-        run: apt-get update && apt-get install -y python3.11 python3-pip python3.11-venv
+        run: apt-get update && apt-get install -y python3.11 python3-pip python3.11-venv python3-debian
 
       - name: "Download binary"
         uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4.3.0
@@ -1932,6 +1932,11 @@ jobs:
       - name: "Validate global Python install"
         run: python3.11 scripts/check_system_python.py --uv ./uv --externally-managed
 
+      - name: "Test `uv run` with system Python"
+        run: |
+          ./uv run -p python3.11 -v python -c "import debian"
+          ./uv run -p python3.11 -v --with anyio python -c "import debian"
+
   system-test-fedora:
     timeout-minutes: 10
     needs: build-binary-linux-libc