Merge refactor/config-deerflow-context into release/2.0-rc

Cherry-pick PR #2271's config refactor onto release/2.0-rc.
Used 'git merge -X theirs' to auto-resolve content conflicts in favor of
the PR's design (frozen AppConfig + explicit-parameter passing).

Limitations:
- Release-only changes that overlapped with PR's refactor in 119 files
  are NOT preserved — those files reflect PR's version. Follow-up commits
  on this branch will need to re-apply release-only modifications where
  meaningful.
- See PR #2271 for design rationale.

config.example.yaml

@@ -816,14 +816,10 @@ skill_evolution:
 # Unified storage backend for LangGraph checkpointer and DeerFlow
 # application data (runs, threads metadata, feedback, etc.).
 #
-# backend: memory  -- No persistence, data lost on restart
+# backend: memory  -- No persistence, data lost on restart (default)
 # backend: sqlite  -- Single-node deployment, files in sqlite_dir
 # backend: postgres -- Production multi-node deployment
 #
-# If this section is omitted or empty in config.yaml, DeerFlow uses:
-#   backend: sqlite
-#   sqlite_dir: .deer-flow/data
-#
 # SQLite mode uses a single deerflow.db file with WAL journal mode
 # for both checkpointer and application data.
 #