Move citation protocol injection to the system layer so custom prompts no
longer own citation syntax. Agents can disable inline citations while source
aliases still encode and decode tool arguments correctly.
Replace raw chunk/document/KB IDs in LLM context with short cN/dN/bN/wN
aliases, decode tool arguments on the way in, and expand compact <ref/>
citations to the public <kb>/<web> format before user-facing output.
wizardchen