fix(core): allow question tool by default for primary-mode agents #372

Acceptance Criteria

• A config-defined agent with mode: primary (no question in its config) resolves with the question tool allowed.
• A config-defined agent with mode: subagent still resolves with question denied.
• A config-defined agent with an explicit question: deny in its config keeps the explicit deny (config wins over the new default).
• Hidden native agents (compaction, title, summary) are unaffected — no implicit question allow appears.
• Native build and plan behavior is unchanged.

Testing Decisions

Extend the existing agent-registry tests (the suite that covers config-defined agents and permission merging). No new suite; this is a small extension of covered surface.

Key Decisions

• Normalize after the config-agent loop, when each agent's final mode is known — the pass must see card/user mode overrides, not pre-loop defaults.
• Treat "explicit rule exists" the same way the existing external_directory normalization pass does (scan the resolved permission rules for a question rule), so wildcard-only configs still get the grant.
• Deny remains the default for mode: subagent — asking a question from a cast subagent deadlocks the loop.

Constraints & Invariants

• User/card config is the highest authority: an explicit question rule in config must never be clobbered by the normalization pass.
• No behavior change for clients where the question tool isn't in the registry (tool availability gating elsewhere stays as-is).

Prior Art

• The agent registry's existing post-loop normalization pass for external_directory — same pattern (scan rules, conditional merge).
• The native build/plan definitions, which already merge question: "allow" on top of defaults.

Notes

Found while wiring Amico director mode cards: the develop/research mode-card agents (config-defined, mode: primary) could not use the question tool while build/plan could. The card fix (explicit question: allow in card frontmatter) is tracked separately in harmoniqs/amicode as belt-and-braces; this issue is the harness-level fix so any future primary agent gets the interview flow by default.