fix the bug for file segmentation

Author: Zongwei9888

mcp_agent.config.yaml

@@ -1,90 +1,102 @@
 $schema: ./schema/mcp-agent.config.schema.json
-anthropic: null
-default_search_server: brave
+
+# Default search server configuration
+# Options: "brave" or "bocha-mcp"
+default_search_server: "brave"
+
+# Planning mode configuration
+# Options: "segmented" or "traditional"
+# segmented: Breaks down large tasks to avoid token truncation (recommended)
+# traditional: Uses parallel agents but may hit token limits
+planning_mode: "traditional"
+
+# Document segmentation configuration
 document_segmentation:
-  enabled: true
-  size_threshold_chars: 50000
+  enabled: false  # Whether to use intelligent document segmentation
+  size_threshold_chars: 50000  # Document size threshold (in characters) to trigger segmentation
+  # If document size > threshold and enabled=true, use segmentation workflow
+  # If document size <= threshold or enabled=false, use traditional full-document reading
+
 execution_engine: asyncio
 logger:
+  transports: [console, file]
   level: info
-  path_settings:
-    path_pattern: logs/mcp-agent-{unique_id}.jsonl
-    timestamp_format: '%Y%m%d_%H%M%S'
-    unique_id: timestamp
   progress_display: true
-  transports:
-  - console
-  - file
+  path_settings:
+    path_pattern: "logs/mcp-agent-{unique_id}.jsonl"
+    unique_id: "timestamp" # Options: "timestamp" or "session_id"
+    timestamp_format: "%Y%m%d_%H%M%S"
+
+
+
 mcp:
   servers:
-    bocha-mcp:
-      args:
-      - tools/bocha_search_server.py
-      command: python3
-      env:
-        BOCHA_API_KEY: ''
-        PYTHONPATH: .
     brave:
-      args:
-      - -y
-      - '@modelcontextprotocol/server-brave-search'
-      command: npx
+      # On windows replace the command and args line to use `node` and the absolute path to the server.
+      # Use `npm i -g @modelcontextprotocol/server-brave-search` to install the server globally.
+      # Use `npm -g root` to find the global node_modules path.`
+      # command: "node"
+      # args: ["c:/Program Files/nodejs/node_modules/@modelcontextprotocol/server-brave-search/dist/index.js"]
+      command: "npx"
+      args: ["-y", "@modelcontextprotocol/server-brave-search"]
       env:
-        BRAVE_API_KEY: ''
-    code-implementation:
-      args:
-      - tools/code_implementation_server.py
-      command: python
-      description: Paper code reproduction tool server - provides file operations,
-        code execution, search and other functions
+        # You can also place your BRAVE_API_KEY in the fastagent.secrets.yaml file.
+        BRAVE_API_KEY: ""
+    filesystem:
+      # On windows update the command and arguments to use `node` and the absolute path to the server.
+      # Use `npm i -g @modelcontextprotocol/server-filesystem` to install the server globally.
+      # Use `npm -g root` to find the global node_modules path.`
+      # command: "node"
+      # args: ["c:/Program Files/nodejs/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js","."]
+      command: "npx"
+      args: ["-y", "@modelcontextprotocol/server-filesystem"]
+    fetch:
+      command: "uvx"
+      args: ["mcp-server-fetch"]
+    github-downloader:
+      command: "python"
+      args: ["tools/git_command.py"]
       env:
-        PYTHONPATH: .
-    code-reference-indexer:
-      args:
-      - tools/code_reference_indexer.py
-      command: python
-      description: Code reference indexer server - Provides intelligent code reference
-        search from indexed repositories
+        PYTHONPATH: "."
+    file-downloader:
+      command: "python"
+      args: ["tools/pdf_downloader.py"]
       env:
-        PYTHONPATH: .
+        PYTHONPATH: "."
     command-executor:
-      args:
-      - tools/command_executor.py
-      command: python
+      command: "python"
+      args: ["tools/command_executor.py"]
       env:
-        PYTHONPATH: .
-    document-segmentation:
-      args:
-      - tools/document_segmentation_server.py
-      command: python
-      description: Document segmentation server - Provides intelligent document analysis
-        and segmented reading to optimize token usage
+        PYTHONPATH: "."
+    code-implementation:
+      command: "python"
+      args: ["tools/code_implementation_server.py"]
       env:
-        PYTHONPATH: .
-    fetch:
-      args:
-      - mcp-server-fetch
-      command: uvx
-    file-downloader:
-      args:
-      - tools/pdf_downloader.py
-      command: python
+        PYTHONPATH: "."
+      description: "Paper code reproduction tool server - provides file operations, code execution, search and other functions"
+    code-reference-indexer:
+      command: "python"
+      args: ["tools/code_reference_indexer.py"]
       env:
-        PYTHONPATH: .
-    filesystem:
-      args:
-      - -y
-      - '@modelcontextprotocol/server-filesystem'
-      command: npx
-    github-downloader:
-      args:
-      - tools/git_command.py
-      command: python
+        PYTHONPATH: "."
+      description: "Code reference indexer server - Provides intelligent code reference search from indexed repositories"
+    bocha-mcp:
+      command: "python3"
+      args: ["tools/bocha_search_server.py"]
       env:
-        PYTHONPATH: .
+        PYTHONPATH: "."
+        BOCHA_API_KEY: ""
+    document-segmentation:
+      command: "python"
+      args: ["tools/document_segmentation_server.py"]
+      env:
+        PYTHONPATH: "."
+      description: "Document segmentation server - Provides intelligent document analysis and segmented reading to optimize token usage"
+
 openai:
+  # Secrets (API keys, etc.) are stored in an mcp_agent.secrets.yaml file which can be gitignored
+  #  default_model: "o3-mini"
   default_model: "anthropic/claude-sonnet-4"
-planning_mode: traditional
+
 
 anthropic:
-  default_model: ""

utils/llm_utils.py

@@ -187,6 +187,12 @@ def get_adaptive_agent_config(
             config["algorithm_analysis"].append("document-segmentation")
         if "document-segmentation" not in config["code_planner"]:
             config["code_planner"].append("document-segmentation")
+    else:
+        config["concept_analysis"] = ["filesystem"]
+        if "filesystem" not in config["algorithm_analysis"]:
+            config["algorithm_analysis"].append("filesystem")
+        if "filesystem" not in config["code_planner"]:
+            config["code_planner"].append("filesystem")
 
     return config