feat: Remove deprecated tools from built-in agents configuration

- Eliminated the "thinking" and "todo_write" tools from the allowed tools list in multiple sections of the `builtin_agents.yaml` file, streamlining the agent capabilities.
- This change enhances the clarity and relevance of the tools available to built-in agents, ensuring a more focused and efficient configuration.

config/builtin_agents.yaml

@@ -75,8 +75,6 @@ builtin_agents:
       kb_selection_mode: "all"
       retrieve_kb_only_when_mentioned: false
       allowed_tools:
-        - "thinking"
-        - "todo_write"
         - "knowledge_search"
         - "grep_chunks"
         - "list_knowledge_chunks"
@@ -128,8 +126,6 @@ builtin_agents:
         - "csv"
         - "xlsx"
       allowed_tools:
-        - "thinking"
-        - "todo_write"
         - "data_schema"
         - "data_analysis"
       web_search_enabled: false
@@ -172,8 +168,6 @@ builtin_agents:
       kb_selection_mode: "all"
       retrieve_kb_only_when_mentioned: false
       allowed_tools:
-        - "thinking"
-        - "todo_write"
         - "wiki_search"
         - "wiki_read_page"
         - "wiki_read_source_doc"
@@ -219,8 +213,6 @@ builtin_agents:
       retrieve_kb_only_when_mentioned: false
       retain_retrieval_history: true
       allowed_tools:
-        - "thinking"
-        - "todo_write"
         - "wiki_search"
         - "wiki_read_page"
         - "wiki_read_source_doc"