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* fix(config): upgrade the config.yaml the Gateway loads scripts/config-upgrade.sh resolved DEER_FLOW_CONFIG_PATH, then backend/config.yaml, then <checkout>/config.yaml. make dev exports DEER_FLOW_PROJECT_ROOT=<checkout>, so the Gateway reads the checkout copy first: with both files present the script upgraded a file nothing loads and left the live config outdated while reporting success. It also ignored DEER_FLOW_PROJECT_ROOT and a DEER_FLOW_CONFIG_PATH set in .env, and fell back to another file when DEER_FLOW_CONFIG_PATH named a missing one. Ask the harness resolver (AppConfig.resolve_config_path) instead of copying its order, defaulting DEER_FLOW_PROJECT_ROOT to the checkout as serve.sh does. A missing DEER_FLOW_CONFIG_PATH or invalid project root now fails with the Gateway's error; no config anywhere still creates <checkout>/config.yaml from the example. * docs(changelog): reference #5991 * test(config): pin config-upgrade seeding a missing config from the example --------- Co-authored-by: Willem Jiang <willem.jiang@gmail.com>