fix(v1): isolate Bash commands from harness venv

[eigenpaul]

Fixes #2250

This PR runs Bash subprocesses with a copy of the controller environment that removes VIRTUAL_ENV and the harness added PATH entries. The controller environment itself is unchanged.

Verified in a Prime python:3.11-slim sandbox:

command -v python3
python3 --version
command -v pip
command -v pip3
python3 -m pip --version

Current main:

/root/.cache/uv/environments-v2/<environment-id>/bin/python3
Python 3.11.15
/usr/local/bin/pip
/usr/local/bin/pip3
/root/.cache/uv/environments-v2/<environment-id>/bin/python3: No module named pip

With this patch:

/usr/local/bin/python3
Python 3.11.15
/usr/local/bin/pip
/usr/local/bin/pip3
pip 24.0 from /usr/local/lib/python3.11/site-packages/pip (python 3.11)

#2011 identified the same root cause but that PR targets the old default harness path.

---

Note

Low Risk
Small, localized change to bash tool env handling with no auth or data-path impact; main risk is edge cases if PATH stripping is incomplete on unusual layouts.

Overview
Bash tool subprocesses no longer inherit the harness’s uv virtualenv. run_bash now runs bash -c with a copied environment that drops VIRTUAL_ENV and strips the harness-added PATH prefix ({venv}/bin and $HOME/.local/bin), so agent commands resolve to the sandbox’s system Python and pip instead of the controller interpreter.

The harness process environment is unchanged; only the bash tool’s child process gets the sanitized copy.

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Note

Isolate Bash harness subprocess execution from the harness virtualenv

The run_bash helper in program.py now strips harness virtualenv paths from the subprocess environment before running user commands. It removes VIRTUAL_ENV and strips the leading venv and ~/.local/bin entries from PATH, so user scripts resolve executables from the system environment rather than the harness venv. Risk: changes which executables are resolved for any bash command run through this harness.

^{Macroscope summarized 87f3994.}