fix(harness): resolve runtime paths from project root (#2642)

* fix(harness): resolve runtime paths from project root

* docs(config): update

* fix(config): address runtime path review feedback

* test(config): fix skills path e2e root

* test(config): cover legacy config fallback when project root lacks config files

Verifies that when DEER_FLOW_PROJECT_ROOT is unset and cwd has no
config.yaml/extensions_config.json, AppConfig and ExtensionsConfig fall back
to the legacy backend/repo-root candidates — the backward-compat path
requested in PR #2642 review.

---------

Co-authored-by: Willem Jiang <willem.jiang@gmail.com>

config.example.yaml

@@ -2,8 +2,11 @@
 #
 # Guidelines:
 # - Copy this file to `config.yaml` and customize it for your environment
-# - The default path of this configuration file is `config.yaml` in the current working directory.
-#   However you can change it using the `DEER_FLOW_CONFIG_PATH` environment variable.
+# - The default path of this configuration file is `config.yaml` in the project root.
+#   You can set `DEER_FLOW_PROJECT_ROOT` to define that root explicitly, or use
+#   `DEER_FLOW_CONFIG_PATH` to point at a specific config file.
+# - Runtime state defaults to `.deer-flow` under the project root. Override it
+#   with `DEER_FLOW_HOME` when you need a different writable data directory.
 # - Environment variables are available for all field values. Example: `api_key: $OPENAI_API_KEY`
 # - The `use` path is a string that looks like "package_name.sub_package_name.module_name:class_name/variable_name".
 
@@ -678,7 +681,8 @@ sandbox:
 
 skills:
   # Path to skills directory on the host (relative to project root or absolute)
-  # Default: ../skills (relative to backend directory)
+  # Default: skills under the project root
+  # Override with DEER_FLOW_SKILLS_PATH when this field is omitted.
   # Uncomment to customize:
   # path: /absolute/path/to/custom/skills