CLI --json flag is ignored by most subcommands; output mode still tied to cli.mode=agent

[RandomOscillations]

Summary

The global --json flag is advertised at root (extropy --help) and in docs as a per-command machine-output override, but most command handlers ignore it and only honor cli.mode=agent.

Repro

1. Set human mode:

extropy config set cli.mode human

2. Run inside a valid study:

cd examples/study-02
extropy --json results summary

3. Observe output is human-formatted text, not JSON.

Additional behavior:

• extropy results --json fails with No such option: --json (Click/Typer global option placement behavior).
• Some error paths (e.g., outside-study DB resolution in query) print rich text errors even when --json is passed.

Expected

• --json should force JSON output regardless of cli.mode.
• Error paths should also return structured JSON in JSON mode.
• Docs/UX should clearly reflect whether --json must be root-level (extropy --json <cmd>) or accepted on subcommands.

Likely Root Cause

Most command modules derive output mode via is_agent_mode() only, instead of get_json_mode() or is_agent_mode().

Observed references:

• extropy/cli/commands/{results,query,sample,network,scenario,persona,spec,simulate,chat}.py
• extropy/cli/commands/validate.py already uses helper logic combining both modes.

Suggested Fix

1. Introduce common helper (e.g. _json_enabled()) in CLI layer: get_json_mode() or is_agent_mode().
2. Replace command-local agent_mode = is_agent_mode() with helper.
3. Route early resolver failures (study detection, etc.) through Output in JSON mode.
4. Add regression tests:
   • cli.mode=human + root --json returns JSON for representative commands.
   • outside-study errors return JSON when --json passed.
5. Update docs to clarify root option placement (extropy --json <command>) and/or add per-command passthrough if desired.

Severity

Medium-high (automation contract regression). Not simulation-core blocking, but breaks non-interactive pipelines that depend on explicit --json overrides.

[RandomOscillations]

Temporary mitigation applied:

• CLI --json option has been removed from the public surface (not shown in help; passing it now errors).
• Internal JSON-mode logic is intentionally retained in code for later restoration.

Reason: avoid exposing a broken override path while we address full cross-command parity (get_json_mode() or is_agent_mode() + JSON-safe error paths).

Issue remains open for the real fix.