folder name changes

Author: TorkelE

docs/pages.jl

@@ -1,32 +1,32 @@
 pages = Any[
     "Home" => "home.md",
     "Introduction to Catalyst" => Any[
-        "01_introduction_to_catalyst/01_catalyst_for_new_julia_users.md",
-        "01_introduction_to_catalyst/02_introduction_to_catalyst.md"
+        "introduction_to_catalyst/catalyst_for_new_julia_users.md",
+        "introduction_to_catalyst/introduction_to_catalyst.md"
         # Advanced introduction.
     ],
     "Model Creation and Properties" => Any[
-        "02_model_creation/01_dsl_description.md",
+        "model_creation/dsl_description.md",
         # DSL - Advanced
-        "02_model_creation/03_programmatic_CRN_construction.md",
-        "02_model_creation/04_constraint_equations.md",
-        "02_model_creation/05_compositional_modeling.md",
+        "model_creation/programmatic_CRN_construction.md",
+        "model_creation/constraint_equations.md",
+        "model_creation/compositional_modeling.md",
         # Events.
         # Distributed parameters, rates, and initial conditions.
         # Loading and writing models to files.
         # Model visualisation.
-        "02_model_creation/10_network_analysis.md",
-        "02_model_creation/11_chemistry_related_functionality.md",
+        "model_creation/network_analysis.md",
+        "model_creation/chemistry_related_functionality.md",
         "Model creation examples" => Any[
-            "02_model_creation/examples/basic_CRN_examples.md",
-            "02_model_creation/examples/hodgkin_huxley_equation.md",
-            "02_model_creation/examples/smoluchowski_coagulation_equation.md"
+            "model_creation/examples/basic_CRN_examples.md",
+            "model_creation/examples/hodgkin_huxley_equation.md",
+            "model_creation/examples/smoluchowski_coagulation_equation.md"
         ]
     ],
     "Model simulation" => Any[
         # Simulation introduction.
         # Simulation plotting.
-        "03_model_simulation/03_simulation_structure_interfacing.md",
+        "model_simulation/simulation_structure_interfacing.md",
         # Monte Carlo/Ensemble simulations.
         # Stochastic simulation statistical analysis.
         # ODE Performance considerations/advice.
@@ -35,24 +35,24 @@ pages = Any[
         # Finite state projection
     ],
     "Steady state analysis" => Any[
-        "04_steady_state_functionality/01_homotopy_continuation.md",
-        "04_steady_state_functionality/02_nonlinear_solve.md",
+        "steady_state_functionality/homotopy_continuation.md",
+        "steady_state_functionality/nonlinear_solve.md",
         # Stability analysis.
-        "04_steady_state_functionality/04_bifurcation_diagrams.md"
+        "steady_state_functionality/bifurcation_diagrams.md"
         # Dynamical systems analysis.
     ],
     "Inverse Problems" => Any[
         # Inverse problems introduction.
-        "05_inverse_problems/02_optimization_ode_param_fitting.md",
-        # "inverse_problems/03_petab_ode_param_fitting.md",
+        "inverse_problems/optimization_ode_param_fitting.md",
+        # "inverse_problems/petab_ode_param_fitting.md",
         # ODE parameter fitting using Turing.
         # SDE/Jump fitting.
         # Non-parameter fitting optimisation.
-        "05_inverse_problems/07_structural_identifiability.md",
+        "inverse_problems/07_structural_identifiability.md",
         # Practical identifiability.
         # GLobal and local sensitivity analysis.
         "Inverse problem examples" => Any[
-            "05_inverse_problems/examples/ode_fitting_oscillation.md"
+            "inverse_problems/examples/ode_fitting_oscillation.md"
         ]
     ],
     "Spatial modelling" => Any[