refactor(typing): Fixup typing A2 - workflow engine & nodes (#31723)

Co-authored-by: gemini-code-assist[bot] <176961590+gemini-code-assist[bot]@users.noreply.github.com>
Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com>
Co-authored-by: Asuka Minato <i@asukaminato.eu.org>

api/ty.toml

@@ -1,16 +1,15 @@
 [src]
 exclude = [
     # deps groups (A1/A2/B/C/D/E)
-    # A2: workflow engine/nodes
-    "core/workflow",
-    "core/app/workflow",
-    "core/helper/code_executor",
     # B: app runner + prompt
     "core/prompt",
     "core/app/apps/base_app_runner.py",
     "core/app/apps/workflow_app_runner.py",
+    "core/agent",
+    "core/plugin",
     # C: services/controllers/fields/libs
     "services",
+    "controllers/inner_api",
     "controllers/console/app",
     "controllers/console/explore",
     "controllers/console/datasets",
@@ -28,3 +27,8 @@ exclude = [
     "tests",
 ]
 
+
+[rules]
+deprecated = "ignore"
+unused-ignore-comment = "ignore"
+# possibly-missing-attribute = "ignore"