Refactor AGENTS.md §15 to resolve Knowledge Base tool hierarchy conflict

Context

The swarm architecture documentation was recently consolidated, moving the startup workflow into AGENTS.md. A core mandate is the "Anti-Hallucination Policy", which dictates the usage of Knowledge Base tools.

Problem

There is a split-brain conflict within AGENTS.md regarding the primary Knowledge Base tool.

• §2.1 correctly establishes ask_knowledge_base as the primary Anti-Hallucination tool for conceptual understanding (acting as an embedded zero-cost RAG agent) and demotes query_documents to file discovery.
• However, §15.1 ("The Query Command") and §15.3 ("The Two-Stage Query Protocol") still contain legacy instructions that incorrectly promote query_documents as the "most important tool" and mandate its use for Stage 1 (understanding the technical "how").

This conflict creates cognitive friction for agents, as they receive contradictory instructions on how to acquire context, leading to inefficient query_documents -> view_file chains instead of utilizing the superior ask_knowledge_base synthesis.

Architectural Reality

ask_knowledge_base is strictly superior for conceptual queries. It performs the same underlying vector search as query_documents but adds an LLM synthesis step, returning both the answer and the same top-5 ranked references. Using query_documents for conceptual understanding wastes context window and turns.

Fix

Refactor AGENTS.md to establish a unified, non-contradictory tool hierarchy:

1. Rewrite §15.1 to reflect the dominance of ask_knowledge_base and align with §2.1.
2. Update §15.3 (Stage 1) to mandate ask_knowledge_base for "understanding the how", reserving query_documents for exhaustive path enumeration.
3. Ensure the documentation consistently promotes the Embedded RAG pattern over manual file reading for conceptual tasks.

Acceptance Criteria

• §15.1 no longer claims query_documents is the "most important tool".
• §15.3 instructs the use of ask_knowledge_base for Stage 1 conceptual queries.
• The overall document is internally consistent with the hierarchy defined in §2.1.
• Any references to manual query_documents -> view_file chains for conceptual understanding are removed.