refactor(conductor): refine Plan Mode terminology to avoid confusion with native CLI mode

[fernandomenuk]

Description

This PR refines the internal terminology used within Conductor's orchestration protocols to clearly distinguish it from Gemini CLI's native "Plan Mode" feature.

Why?

Gemini CLI recently introduced a native "Plan Mode" designed for read-only research and pre-flight planning. Conductor, which manages its own "Spec & Plan" lifecycle, previously used the term "Plan Mode" to describe its internal orchestration state. This collision in terminology can lead to:

1. User Confusion: Users might believe Conductor is toggling the native CLI feature rather than its own internal state.
2. Model Confusion: The AI agent may conflate Conductor's active orchestration instructions with the native CLI's read-only restrictions.

Changes

• Refined Terminology: Renamed "PLAN MODE PROTOCOL" to "CONDUCTOR OPERATIONAL PROTOCOL (INTERNAL PLANNING STATE)" in setup.toml and newTrack.toml.
• Clarified tool calls: Updated descriptions for enter_plan_mode and exit_plan_mode to refer to initiating/finalizing an "Internal Orchestration State".
• Explicit Differentiation: Added notes within the prompts to explicitly state that this state is separate from the Gemini CLI's native Plan Mode.
• Policy Comments: Updated comments in policies/conductor.toml for consistency.