## Related issue
[OMNI-3489](https://linear.app/omnigent/issue/OMNI-3489/honor-omnidev-state-and-config-directories-in-omnigent-cli-paths)
## Summary
- Prevent `omnidev omnigent …` commands from leaking auth tokens, session logs, host daemon records, and native harness launch state into the developer's real `~/.omnigent` directory.
- Make runtime state honor `OMNIGENT_DATA_DIR` while configuration independently honors `OMNIGENT_CONFIG_HOME`; harness-specific native-state overrides still take precedence.
- Keep the real `HOME` and `XDG_*` environment intact so harness credentials and caches remain available, and update REPL E2E setup to seed its theme in the effective config without clobbering mock auth.
**ELI5:** omnidev already gives each development pod its own labeled storage boxes, but some Omnigent code still put files in the user's shared box. Those paths now use the pod's boxes without moving the user's home directory.
```text
omnidev omnigent
|
+-- OMNIGENT_DATA_DIR ------> tokens, logs, host/native state
+-- OMNIGENT_CONFIG_HOME ---> config.yaml
+-- HOME / XDG_* ------------> unchanged credentials and caches
```
## Test Plan
- `uv run --frozen pytest tests/frontends/sdk/test_user_config.py`
- `uv run --frozen pytest tests/test_native_state_legacy_dirs.py`
- `uv run --frozen pytest tests/host/test_cli_host.py::test_host_pid_path_honors_data_dir_at_import`
- `uv run --frozen pytest tests/e2e/omnigent/test_pexpect_harness.py`
- `uv run --frozen pytest tests/e2e/omnigent/test_repl_smoke.py::test_repl_smoke_single_prompt`
- `cargo test --manifest-path dev/omnidev/Cargo.toml omnigent_cmd::tests`
- `uv run --frozen ruff check omnigent/claude_native_state.py omnigent/cli.py omnigent/cli_auth.py omnigent/codex_native_state.py omnigent/opencode_native_state.py omnigent/repl/_session_log.py sdks/ui/omnigent_ui_sdk/terminal/_config.py tests/frontends/sdk/test_user_config.py tests/host/test_cli_host.py tests/test_native_state_legacy_dirs.py tests/e2e/omnigent/_pexpect_harness.py tests/e2e/omnigent/test_pexpect_harness.py`
- `cargo fmt --manifest-path dev/omnidev/Cargo.toml --check`
## Demo
N/A — non-visual CLI state-isolation fix.
## Type of change
- [x] Bug fix
- [ ] Feature
- [ ] UI / frontend change
- [ ] Refactor / chore
- [ ] Docs
- [ ] Test / CI
- [ ] Breaking change
## Test coverage
- [x] Unit tests added / updated
- [ ] Integration tests added / updated
- [x] E2E tests added / updated
- [ ] Manual verification completed
- [ ] Existing tests cover this change
- [ ] Not applicable
## Coverage notes
Regression tests cover pod environment wiring, data/config override precedence, HOME fallbacks, host pidfile placement, native harness state roots, and REPL startup with an isolated config home.
## Changelog
`omnidev omnigent` commands now keep runtime state and configuration inside their development pod.
Signed-off-by: Zeyi (Rice) Fan <zeyi.f@databricks.com>
Zeyi (Rice) Fan
08b20956f2