diff --git a/dify-agent/src/dify_agent/adapters/llm/model.py b/dify-agent/src/dify_agent/adapters/llm/model.py
index 02b0f71b464..1f4c93a161e 100644
--- a/dify-agent/src/dify_agent/adapters/llm/model.py
+++ b/dify-agent/src/dify_agent/adapters/llm/model.py
@@ -343,7 +343,8 @@ def _map_model_request_to_prompt_messages(message: ModelRequest) -> list[PromptM
 
     for part in message.parts:
         if isinstance(part, SystemPromptPart):
-            prompt_messages.append(SystemPromptMessage(content=part.content))
+            if part.content.strip():
+                prompt_messages.append(SystemPromptMessage(content=part.content))
         elif isinstance(part, UserPromptPart):
             prompt_messages.append(UserPromptMessage(content=_map_user_prompt_content(part.content)))
         elif isinstance(part, ToolReturnPart):
diff --git a/dify-agent/src/dify_agent/layers/shell/layer.py b/dify-agent/src/dify_agent/layers/shell/layer.py
index 2e39185aa64..163680451eb 100644
--- a/dify-agent/src/dify_agent/layers/shell/layer.py
+++ b/dify-agent/src/dify_agent/layers/shell/layer.py
@@ -301,6 +301,8 @@ class DifyShellLayer(PydanticAILayer[DifyShellLayerDeps, object, DifyShellLayerC
         self._clear_tracked_jobs()
 
     async def _tool_run(self, script: str, timeout: float = DEFAULT_TIMEOUT_SECONDS) -> ShellRunToolResult:
+        """Start a shell job in the current workspace and return its output and status."""
+
         try:
             env = self._build_shell_command_env(include_agent_stub_env=True)
             agent_stub_token = env.get(AGENT_STUB_AUTH_JWE_ENV_VAR)
@@ -337,6 +339,8 @@ class DifyShellLayer(PydanticAILayer[DifyShellLayerDeps, object, DifyShellLayerC
             return _tool_unexpected_error("shell_run", exc)
 
     async def _tool_wait(self, job_id: str, timeout: float = DEFAULT_TIMEOUT_SECONDS) -> ShellRunToolResult:
+        """Wait for more output or completion from an existing shell job."""
+
         try:
             offset = self._tracked_offset(job_id)
             result = await self._require_resource().commands.wait(job_id, offset=offset, timeout=timeout)
@@ -369,6 +373,8 @@ class DifyShellLayer(PydanticAILayer[DifyShellLayerDeps, object, DifyShellLayerC
             return _tool_unexpected_error("shell_wait", exc, job_id=job_id)
 
     async def _tool_input(self, job_id: str, text: str, timeout: float = DEFAULT_TIMEOUT_SECONDS) -> ShellRunToolResult:
+        """Send text to a running shell job and wait for its next output."""
+
         try:
             offset = self._tracked_offset(job_id)
             result = await self._require_resource().commands.input(job_id, text, offset=offset, timeout=timeout)
@@ -405,6 +411,8 @@ class DifyShellLayer(PydanticAILayer[DifyShellLayerDeps, object, DifyShellLayerC
         job_id: str,
         grace_seconds: float = DEFAULT_TERMINATE_GRACE_SECONDS,
     ) -> ShellInterruptToolResult:
+        """Interrupt a running shell job and return its final status."""
+
         try:
             self._ensure_tracked_job(job_id)
             result = await self._require_resource().commands.interrupt(job_id, grace_seconds=grace_seconds)
diff --git a/dify-agent/tests/local/dify_agent/adapters/llm/test_model.py b/dify-agent/tests/local/dify_agent/adapters/llm/test_model.py
index 589e420bf80..eb6df382054 100644
--- a/dify-agent/tests/local/dify_agent/adapters/llm/test_model.py
+++ b/dify-agent/tests/local/dify_agent/adapters/llm/test_model.py
@@ -101,6 +101,7 @@ class DifyLLMAdapterModelTests(unittest.IsolatedAsyncioTestCase):
         messages = [
             ModelRequest(
                 parts=[
+                    SystemPromptPart("   "),
                     SystemPromptPart("request system"),
                     UserPromptPart("hello"),
                     ToolReturnPart(
diff --git a/dify-agent/tests/local/dify_agent/layers/shell/test_layer.py b/dify-agent/tests/local/dify_agent/layers/shell/test_layer.py
index 0ffc47c9bd8..ae75ff1aea0 100644
--- a/dify-agent/tests/local/dify_agent/layers/shell/test_layer.py
+++ b/dify-agent/tests/local/dify_agent/layers/shell/test_layer.py
@@ -303,6 +303,15 @@ def test_shell_type_id_constant_matches_implementation_class() -> None:
     assert DIFY_SHELL_LAYER_TYPE_ID == DifyShellLayer.type_id
 
 
+def test_shell_layer_tools_have_non_empty_descriptions() -> None:
+    layer = DifyShellLayer.from_config_with_settings(DifyShellLayerConfig())
+
+    descriptions = {tool.name: tool.description for tool in layer.tools}
+
+    assert set(descriptions) == {"shell_run", "shell_wait", "shell_input", "shell_interrupt"}
+    assert all(description and description.strip() for description in descriptions.values())
+
+
 def test_shell_prefix_prompt_describes_workspace_as_temp_space() -> None:
     prompt = shell_layer_module._SHELL_LAYER_PREFIX_PROMPT