fix(cli): preserve one-shot isolation flags

[hzhaoy]

Summary

• Apply isolation env setup before chat and top-level one-shot startup discovery, while keeping _apply_safe_mode(args) as the safe-mode helper.
• Make hermes_cli.config.load_config() honor HERMES_IGNORE_USER_CONFIG=1, skipping the user config.yaml while preserving built-in defaults and managed-scope config.
• Thread ignore_rules into the one-shot runner so AIAgent skips context files and persistent memory for --ignore-rules / --safe-mode.
• Preserve current -z --usage-file support while adding the new isolation plumbing.
• Add regression coverage for top-level --safe-mode -z, direct one-shot ignore_rules, config-loader user-config isolation, and startup env ordering.

Root Cause

Top-level -z bypassed the cmd_chat path where isolation environment variables were set. The one-shot runner also constructed AIAgent without skip_context_files / skip_memory, so AGENTS.md could still be loaded even when the user requested --ignore-rules or --safe-mode.

After #45300, another related gap remained: HERMES_IGNORE_USER_CONFIG was honored by cli.load_cli_config(), the interactive cli.py loader path, but not by the shared hermes_cli.config.load_config() loader used by startup discovery, MCP, shell hooks, and other config consumers. This PR moves that boundary into load_config() and uses a cache signature sentinel so normal and isolated loads do not reuse each other's cached config.

Rebase Notes

• Merged current origin/main (240afd0b70a016ba17568d597e0f2c32f94f4cfd) and resolved conflicts.
• Preserved main's current one-shot hard-exit cleanup wrapper, stateless-channel declaration, explicit agent/session cleanup, and requested_provider wiring.
• Kept _apply_safe_mode(args) intact.
• Collapsed the separate ignore-user-config / ignore-rules env helpers into _apply_isolation_env(args) so startup call sites have a single ordering-sensitive helper.
• Kept usage_file in the run_oneshot() signature and dispatch calls.

Test Plan

• scripts/run_tests.sh tests/hermes_cli/test_tui_resume_flow.py tests/hermes_cli/test_safe_mode.py tests/hermes_cli/test_ignore_user_config_flags.py tests/hermes_cli/test_config_env_expansion.py tests/hermes_cli/test_managed_scope_config.py tests/hermes_cli/test_managed_scope_regression.py tests/hermes_cli/test_mcp_startup.py (37 passed)
• venv/bin/python -m ruff check hermes_cli/main.py hermes_cli/oneshot.py hermes_cli/config.py tests/hermes_cli/test_tui_resume_flow.py tests/hermes_cli/test_safe_mode.py tests/hermes_cli/test_ignore_user_config_flags.py
• git diff --cached --check -- hermes_cli/main.py hermes_cli/oneshot.py hermes_cli/config.py tests/hermes_cli/test_tui_resume_flow.py tests/hermes_cli/test_safe_mode.py tests/hermes_cli/test_ignore_user_config_flags.py

[teknium1]

Thanks for the focused isolation fix. Static review confirms the premise remains present on current main: top-level one-shot dispatch does not forward isolation state (hermes_cli/main.py:14737), and one-shot agent construction omits skip_context_files / skip_memory (hermes_cli/oneshot.py:393). The shared loader also still merges an existing user config unconditionally (hermes_cli/config.py:6953).

The PR's changes target those exact gaps, including separate isolated config-cache state, without adding model-tool surface or altering conversation context mid-session.

Automated hermes-sweeper review.

[GottZ]

This was generated by AI during triage.

Summary

Two open PRs address the same one-shot isolation gap: user config and rules/memory isolation flags not reaching the embedded agent when invoked via top-level -z/--safe-mode. #51797 (+308/-22) fixes the gap at all three levels named in the root cause — top-level dispatch (main.py), config loader (config.py), and oneshot agent construction (oneshot.py). #73005 (+216/-5) only touches the config-loader and oneshot layers, leaving the top-level dispatch chokepoint untouched.

Related pull requests

• #51797 related — (+308/-22) — keep_open (contributor teknium1, 7327 commits): diff adds _apply_isolation_env() as a chokepoint called from both cmd_chat and _prepare_agent_startup, so top-level -z/--safe-mode sets isolation env vars before plugin/tool discovery; also adds a sentinel cache signature in load_config() for HERMES_IGNORE_USER_CONFIG and threads an explicit ignore_rules parameter through run_oneshot/_run_agent into AIAgent(skip_context_files=, skip_memory=). Reviewer's static check against current main confirmed all three cited gaps (main.py:14737, oneshot.py:393, config.py:6953) are real and are exactly what this diff closes.
• #73005 duplicate — (+216/-5) — no review verdict recorded: diff introduces a shared should_ignore_user_config() helper used by cli.py's load_cli_config() and by _load_config_impl (setting user_sig=None instead of a sentinel signature), and has oneshot._run_agent read HERMES_IGNORE_RULES directly from the env rather than via a passed parameter. It does not modify main.py, so it does not fix the top-level dispatch gap that #51797's reviewer confirmed is still present on current main — meaning -z invocations that never set the env vars in the first place would still leak user config/rules under this PR alone.

Duplicates

#51797 and #73005 both fix the same root cause (isolation flags not reaching load_config()/AIAgent in the one-shot -z path) with overlapping changes to hermes_cli/config.py and hermes_cli/oneshot.py, but #73005 lacks the main.py top-level dispatch fix that #51797 includes.

Suggested consolidation

merge #51797 — the keep_open review from teknium1 (contributor, 7327 commits) verified against current main that its diff closes all three root-cause gaps, including the top-level dispatch chokepoint in main.py that #73005 does not touch. #73005 can be closed as superseded by #51797: it duplicates the config.py/oneshot.py portion of the fix but is incomplete without the main.py change, so merging it alone would not fully resolve the reported issue.

Complex graph

flowchart LR
    classDef open fill:#dbeafe,stroke:#1d4ed8,color:#1e3a8a
    classDef merged fill:#dcfce7,stroke:#15803d,color:#14532d
    classDef closed fill:#e5e7eb,stroke:#6b7280,color:#1f2937
    classDef unverified fill:#f3f4f6,stroke:#9ca3af,color:#374151
    classDef best stroke-width:3px,stroke:#b45309
    classDef target stroke-width:3px,stroke:#4338ca
    subgraph Dup51797 ["PRs duplicating each other"]
        P51797["PR #51797 (open)"]
        P73005["PR #73005 (open)"]
    end
    class P51797 open
    class P73005 open
    class P51797 target
    click P51797 "https://github.com/NousResearch/hermes-agent/pull/51797"
    click P73005 "https://github.com/NousResearch/hermes-agent/pull/73005"

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Graph: solid arrow = fixes / best fix, dashed arrow = partial or unverified (see edge label); boxed group = PRs duplicating each other; amber border = best fix; indigo border = target; gray node = closed or no verify verdict yet (state tag in the node label).

Cross-PR triage: Reviewed 2 pull requests and 0 issues in this complex. Each diff was read against this issue; Assessment working set: 30 kB of PR diffs, 4 kB of issue/PR text, <1 kB of discussion (1 comments), 1 verify verdict. verdicts reflect diff content, not PR titles. Part of an automated triage batch.