完成求解器雅可比矩阵首轮优化，增加更新目录，整理了文档文件夹，增加了服务启动脚本

tests/test_generic_system_xml_simulation.py

@@ -2,6 +2,7 @@ from __future__ import annotations
 
 import asyncio
 import json
+import os
 import threading
 import time
 import unittest
@@ -321,14 +322,18 @@ class GenericSystemXmlSimulationTests(unittest.TestCase):
             if phase == "integrating" and progress >= 0.2:
                 cancel_event.set()
 
-        result = GenericFluidSystem(
-            compile_reactflow_network(chain_project())
-        ).simulate(
-            SolveIVPConfig(t_stop=0.05, method="BDF", max_step=0.001),
-            sample_step=0.005,
-            progress_callback=request_cancel_after_progress,
-            cancel_check=cancel_event.is_set,
-        )
+        with patch.dict(
+            os.environ,
+            {"SIMULATION_ODE_JACOBIAN_MODE": "optimized"},
+        ):
+            result = GenericFluidSystem(
+                compile_reactflow_network(chain_project())
+            ).simulate(
+                SolveIVPConfig(t_stop=0.05, method="BDF", max_step=0.001),
+                sample_step=0.005,
+                progress_callback=request_cancel_after_progress,
+                cancel_check=cancel_event.is_set,
+            )
 
         self.assertFalse(result.success)
         self.assertEqual(result.status, "cancelled")
@@ -343,6 +348,14 @@ class GenericSystemXmlSimulationTests(unittest.TestCase):
         sparsity = integration["jacobianSparsity"]
         self.assertGreater(sparsity["nonzeroCount"], 0)
         self.assertGreater(sparsity["colorGroupCount"], 0)
+        self.assertEqual(
+            integration["jacobian"]["mode"],
+            "scipySparseFiniteDifference",
+        )
+        self.assertEqual(
+            integration["jacobian"]["fallbackReason"],
+            "denseStateDependencyPattern",
+        )
         self.assertEqual(
             integration["totals"]["finiteDifferenceRhsEstimate"],
             sum(