Tutorial updates fixes

Parameter_studies_and_optimization/index.md

@@ -18,5 +18,5 @@ to obtain a desired model behavior.
 Introduction <intro>
 lesson1
 lesson2
-lesson3
+lesson3/lesson3
 ```

Parameter_studies_and_optimization/lesson1.md

@@ -359,6 +359,8 @@ is that this bicycle model has a predefined ankle angle variation
 whereas a real human can compensate for a higher seat by letting the
 ankle operate in a more plantar-flexed position.
 
+### Calculating the metabolism of the muscles with integrals
+
 Before we finish this section, let us take a look at a particularly
 important feature of AnyScript mathematics: The ability to compute
 integral properties. AnyBody has a simple way of approximating the

Parameter_studies_and_optimization/lesson2.md

@@ -399,6 +399,6 @@ picture below:
 
 This completes the introduction to optimization studies.
 
-In {doc}`lesson 3 <lesson3>` we will look at how to use external (3rd. party) optimizers with
+In {doc}`lesson 3 <lesson3/lesson3>` we will look at how to use external (3rd. party) optimizers with
 AnyBody. In particular we will show how to use the Python programming language to run the
 same optimizations as we have done in this Tutorial.

Parameter_studies_and_optimization/python-optimize/BikeModel2D.main.any → Parameter_studies_and_optimization/lesson3/BikeModel2D.main.any

@@ -1,6 +1,4 @@
-#ifnpathexists "../libdef.any"
-#include "<ANYBODY_PATH_INSTALLDIR>/AMMR/libdef.any"
-#endif
+#include "libdef.any"
 
 /**2-D bicyle model.
 Although this model can be rotated in 3-D space it really is just a saggital
@@ -105,7 +103,7 @@ Main = {
     };
     AnyDesVar SaddlePos = {
       Val = Main.BikeParameters.SaddlePos;
-        Min = -0.22 /*-0.03*/;
+        Min = -0.20 /*-0.03*/;
         Max = -0.05;
     };
     AnyDesMeasure MaxAct = {
@@ -129,7 +127,7 @@ Main = {
     };
     AnyDesVar SaddlePos = {
       Val = Main.BikeParameters.SaddlePos;
-        Min = -0.22 /*-0.03*/;
+        Min = -0.20 /*-0.03*/;
         Max = -0.05;
     };
     AnyDesMeasure Metab = {