The developers of pi.dev are geniuses.

They add a --tools flag, which can only add tools onto the built-in tools, so if you wanted to sandbox pi.dev by adding sandboxed versions of the existing tools you will have to run pi.dev via

    pi --no-tools --tools tool1, tool2, tool3

So if you want to sandbox your agent, guess what you'll have to do? Yep, you have to supply --no-extensions.

Here is how to run pi.dev under its most minimal configuration under a sandbox:

    pi --no-tools --no-extensions --tools tool1, tool2, tool3 -e ./your-sandboxing-extension

Sources: https://github.com/earendil-works/pi/issues/555