update agent configs and settings

update query environment settings

improve onboarding, split docling requirements, update ingest and venv scripts

move sync_query into scripts/build and update references

update README with query environment docs and expanded command table

add standalone query environment, update pipeline scripts and config

updated ingest pipeline to docling

refactor pipeline: duckdb layer, query rewrite, forward citation cleanup

new db import

made ingesting with clean-db

fixed ingesting duplicate error and added duckdb rewrite

fixed auto match and linker

fixed forward linker and db cleaning

fixed resolver and improved db merger

Fix author linking bug: add missing lastname_lower field