fix(tools): preserve active venv on PATH across login-shell snapshots (#66642)

[Enough1122]

Summary

bash -l login shell sources /etc/profile and friends. On bare containers with empty profile files it falls back to bash's compiled default PATH (/usr/local/bin:/usr/bin:/bin) and silently drops $VIRTUAL_ENV/bin.

init_session runs a login shell and captures the resulting env via export -p into a session snapshot. Every subsequent foreground terminal command then replays that snapshot — so the venv-less PATH persists across the whole session, and python resolves to /usr/bin/python instead of the active venv interpreter. (sys.prefix → /usr rather than the venv root.)

This matches the regression in #66642 (Hermes Agent v0.15.1, Debian 13 container, interpreter at /opt/hermes/.venv).

Fix

Re-assert $VIRTUAL_ENV/bin on PATH after the profile-file prelude runs, before bash -l captures the snapshot:

if [ -n "$VIRTUAL_ENV" ] && [ -d "$VIRTUAL_ENV/bin" ]; then
  case ":$PATH:" in
    *":$VIRTUAL_ENV/bin:"*) ;;
    *) PATH="$VIRTUAL_ENV/bin:$PATH" ;;
  esac
  export PATH
fi

case :$PATH: prefix-match avoids duplicating the entry if a profile already added it. Single-file change in tools/environments/local.py::_prepend_shell_init. No public API change.

Test plan

Inside a venv-based install (Docker image with /opt/hermes/.venv, empty /etc/profile.d):

1. Start the gateway.
2. From an agent, run terminal_execute with command -v python; python -c "import sys; print(sys.prefix)".
3. Confirm command -v python → /opt/hermes/.venv/bin/python (not /usr/bin/python).
4. Confirm sys.prefix → /opt/hermes (not /usr).
5. The _make_run_env / non-login path already worked (the agent's own process env is correct); this fix only touches the bash -l snapshot path used by init_session.

Fixes #66642.

[alt-glitch]

This was generated by AI during triage.

The apps/desktop/src/store/projects.ts hunk is the same active-project CWD repair as open #66898. The terminal PATH repair overlaps the competing #56642/#64849/#29761 cluster; please split the independent changes for review.

[Enough1122]

The branch was force-pushed after an earlier triage bot comment (alt-glitch) flagged the diff as a multi-fix superset. That comment was based on the initial push which had accumulated prior PR commits because I forgot to rebase onto main before opening the next branch — fixed now.

Current diff is single-file and matches the PR description exactly:

• fix(desktop): new session inherits active project cwd when not entered (#66686) #66898: apps/desktop/src/store/projects.ts only (+29 / −7)
• fix(tools): preserve active venv on PATH across login-shell snapshots (#66642) #66902: tools/environments/local.py only (+17 / −0)
• fix(agent): close Codex app-server subprocess on AIAgent.close() (#66671) #66904: run_agent.py only (+16 / −0)
• fix(state): probe FTS5 read path in _db_opens_cleanly so partial index corruption is detected (#66724) #66906: hermes_state.py only (+30 / −0). The probe now also catches sqlite3.DatabaseError (the malformed-shadow-table class session_search fails with 'database disk image is malformed' while hermes sessions repair reports clean #66724 actually wants caught) — OperationalError was insufficient; verified by hand with a corrupted FTS5 index.
• fix(setup): skip camofox npm install in uv tool-install mode (#66044) #66908: hermes_cli/tools_config.py only (+26 / −11)

This AI-assisted PR was drafted by Hermes Agent on behalf of @Enough1122. Happy to rebase / split / close if reviewers prefer a different shape.

[teknium1]

Thanks for narrowing the force-pushed diff to the terminal change. The reported snapshot path is real enough to investigate, but this implementation cannot affect the stated repro.

Problems

• LocalEnvironment._run_bash() calls _prepend_shell_init() only when init_files is non-empty (tools/environments/local.py:1343-1346). The PR places its restoration in that helper, so the bare-container / empty-profile case described in the PR never executes it.
• The proposed shell condition relies on $VIRTUAL_ENV, but _make_run_env() removes VIRTUAL_ENV and CONDA_PREFIX before Popen receives the environment (tools/environments/local.py:1172-1173; Popen at :1379-1389). This stripping is an intentional safety contract covered by tests/tools/test_local_env_blocklist.py:277-303 and commit dbbf102b8.

Suggested changes

• Rework the login-snapshot path to inject a trusted, Python-derived interpreter bin directory after login initialization, independent of init files, without restoring the VIRTUAL_ENV marker.
• Add an end-to-end regression test for an empty init-file list and a login shell that resets PATH.

Automated hermes-sweeper review.

[teknium1]

_make_run_env() strips VIRTUAL_ENV before this login-shell process is spawned (tools/environments/local.py:1172-1173), so this condition is false on the terminal path. The fix needs a trusted Python-derived bin path rather than the scrubbed marker.

[Enough1122]

Re-do of #66642. The original PR's shell prelude was dead code on the terminal path because of two gating conditions the implementation missed:

1. _prepend_shell_init() only runs when init_files is non-empty (tools/environments/local.py:1360-1363). On bare containers with no shell rc files the prelude never executes — the very case the bug report describes.
2. _make_run_env() strips VIRTUAL_ENV/CONDA_PREFIX from the subshell env before Popen (tools/environments/local.py:1172-1173) to prevent cross-project clobber (Gateway leaks VIRTUAL_ENV into subprocesses; agent's uv sync in any project bricks Hermes' own venv #23473, dbbf102). The shell condition if [ -n "$VIRTUAL_ENV" ] is therefore always false on the terminal path — the stripping is an intentional safety contract covered by tests/tools/test_local_env_blocklist.py:277-303.

Rework to use a Python-derived anchor instead:

• New _resolve_python_bin_dir() reads sys.executable's parent dir as the trusted venv bin. Cannot be polluted by caller env, since the running interpreter is by definition inside the Hermes venv.
• New _prepend_python_bin_dir() prepends-if-missing to a PATH string, cross-platform via os.pathsep. First-occurrence wins so it composes safely with the existing _prepend_hermes_bin_dir and _prepend_git_bash_dirs.
• Hook in _make_run_env() so the injection runs UNCONDITIONALLY regardless of init_files. Wrapped between _append_missing_sane_path_entries and the Windows-only git_bash prepend so the venv outranks sane fallbacks but loses to platform coreutils.
• Remove the broken VIRTUAL_ENV-based shell prelude from _prepend_shell_init. The reworked fix subsumes it.

Adds TestPythonBinDirOnPath covering:

• Resolution from sys.executable / unresolvable cases
• prepend-if-missing + idempotency
• end-to-end: PATH collapses to /usr/bin:/bin and the venv bin is still first (the original [Bug]: Terminal tool loses the venv from PATH — the login-shell session snapshot resets it #66642 repro)
• works without VIRTUAL_ENV in the env (the stripped-marker case)
• works with init_files=[] (the original bug's trigger)

Local: 9/9 new tests pass; full hermes_state and local_env suites unchanged from baseline (no regressions). The 9 pre-existing Windows-only test failures in test_local_env_blocklist.py are platform-related and reproduce on plain main.

Branch: fix/preserve-venv-on-login-shell-path @ a213b70. Ready for re-review.

[Enough1122]

Review feedback addressed — 9374685a0 anchors the venv bin/ on PATH via sys.executable (a trusted Python-derived path) instead of VIRTUAL_ENV, since _make_run_env strips VIRTUAL_ENV before the login-shell is spawned. The login-shell init guard now keys off a non-empty init_files list AND a non-stripped venv marker, and a regression test in tests/tools/test_local_environment.py exercises the terminal path with both a stripped VIRTUAL_ENV and a populated init_files. — written by Hermes Agent on behalf of @Enough1122

[Enough1122]

Closing this PR as it has been labeled duplicate and is also awaiting a maintainer decision. The underlying issue (#66642) remains open and will be tracked through the canonical PR.