fix @ref

docs/developments/julia_structs.qmd

@@ -35,11 +35,11 @@ The `subsurface` part is mapped to the lateral subsurface flow kinematic wave co
 `land` part is mapped the overland flow kinematic wave concept and the `river` part is mapped
 to the river flow kinematic wave concept. Knowledge of this specific mapping is required to
 understand and correctly set input, output and state variables in the TOML configuration file,
-see also [Config and TOML](@ref config_toml). This mapping is described in more detail for each
+see also [Config and TOML](../user_guide/toml_file.qmd). This mapping is described in more detail for each
 model in the section Models. Also the `struct` of each mapped concept is provided, so one can
 check the internal variables in the code. These structs are defined as a parametric composite
 type, with type parameters between curly braces after the `struct` name. See also the next
-paragraph [Vertical and lateral models](@ref) for a more detailed description.
+paragraph [Vertical and lateral models](#vertical-and-lateral-models) for a more detailed description.
 
 ## Vertical and lateral models
 The different model concepts used in wflow are defined as parametric [composite

docs/getting_started/building_a_model.qmd

@@ -11,18 +11,18 @@ model schematization, (dynamic) forcing data, results and states.
 The wflow plugin [hydroMT-wflow](https://github.com/Deltares/hydromt_wflow) of hydroMT can be
 used to build and analyze the following model configurations:
 
-- [wflow\_sbm + kinematic wave routing](../model_docs/model_configurations.html#sbm-kinematic-wave)
-- [wflow\_sbm + local inertial river and floodplain](../model_docs/model_configurations.html#sbm-local-inertial-river)
-- [wflow\_sbm + local inertial river (1D) and land (2D)](../model_docs/model_configurations.html#sbm-local-inertial-river-1d-and-land-2d)
+- [wflow\_sbm + kinematic wave routing](../model_docs/model_configurations.qmd#sbm-kinematic-wave)
+- [wflow\_sbm + local inertial river and floodplain](../model_docs/model_configurations.qmd#sbm-local-inertial-river)
+- [wflow\_sbm + local inertial river (1D) and land (2D)](../model_docs/model_configurations.qmd#sbm-local-inertial-river-1d-and-land-2d)
 - [wflow\_sediment](../model_docs/model_configurations.html#wflow_sediment)
 
 To learn more about the wflow plugin of this Python package, we refer to the [hydroMT-wflow
 documentation](https://deltares.github.io/hydromt_wflow/latest/index.html).
 
 To inspect or modify (for example in QGIS) the netCDF static data of these wflow models it is
 convenient to export the maps to a raster format. This can be done as part of the hydroMT-wflow
-plugin, see also the following [example]
-(https://deltares.github.io/hydromt_wflow/latest/_examples/convert_staticmaps_to_mapstack.html).
+plugin, see also the following
+[example](https://deltares.github.io/hydromt_wflow/latest/_examples/convert_staticmaps_to_mapstack.html).
 It is also possible to create again the netCDF static data file based on the modified raster
 map stack.
 
@@ -31,7 +31,8 @@ map stack.
 The actual data requirements depend on the application of the Model and the Model type. Both
 forcing and static data should be provided in netCDF format, with the same grid definition for
 forcing and static data. The only exception is storage and rating curves for lakes, that should
-be provided in CSV format, see also [Additional settings](@ref).
+be provided in CSV format, see also [Additional settings for
+waterbodies](../model_docs/lateral/waterbodies.qmd#additional-settings).
 
 * Forcing data:
   - Precipitation
@@ -57,65 +58,80 @@ An approach to generate `ldd` data is to make use of the Python package
   data](https://deltares.github.io/pyflwdir/latest/_examples/from_dem.html),
 
 see also Eilander et al. (2021) for more information. Pyflwdir is also used by the
-[hydroMT](@ref) Python package described in the next paragraph. Another approach to generate
-`ldd` data is to make use of PCRaster functionality, see for example
+[hydroMT](https://github.com/Deltares/hydromt) Python package described in the next paragraph.
+Another approach to generate `ldd` data is to make use of PCRaster functionality, see for
+example
 [lddcreate](https://pcraster.geo.uu.nl/pcraster/4.3.1/documentation/pcraster_manual/sphinx/op_lddcreate.html).
 
 Optionally, but also not directly part of a model component are `gauge` locations, that are
 used to extract gridded data from certain locations.
 
 The different supported model configurations are described in the section [Model
-configurations](@ref). Wflow\_sbm models have the vertical concept [SBM](@ref vert_sbm) in
-common and input parameters for this component are described in the [SBM](@ref params_sbm)
-section of Model parameters. For wflow\_sbm models there are two ways to include subsurface
-flow:
-
-1. The kinematic wave approach (see section [Subsurface flow routing](@ref)) as part of the
-   `sbm` model type. Parameters that are part of this component are described in the [Lateral
-   subsurface flow](@ref params_ssf) section of Model parameters. Input parameters for this
-   component are derived from the SBM vertical concept and the land slope. One external
-   parameter [`ksathorfrac`](@ref params_ssf) is used to calculate the horizontal hydraulic
-   conductivity at the soil surface `kh_0`.
-2. Groundwater flow (see section [Groundwater flow component](@ref lateral_gwf)) as part of the
-   `sbm_gwf` model type. For the unconfined aquifer the input parameters are described in the
-   section [Unconfined aquifer](@ref) of Model parameters. The bottom (`bottom`) of the
-   groundwater layer is derived from from the `soilthickness` [mm] parameter of `SBM` and the
-   provided surface elevation `altitude` [m] as part of the static input. The `area` parameter
-   is derived from the model grid. Parameters that are part of the boundary conditions of the
-   unconfined aquifer are listed under [Constant Head](@ref) and [Boundary conditions](@ref) of
-   the Model parameters section.
+configurations](../model_docs/model_configurations.qmd). Wflow\_sbm models have the vertical
+concept [SBM](../model_docs/vertical/sbm.qmd) in common and input parameters for this component
+are described in the [SBM model parameters table](../model_docs/parameters_vertical.qmd#sbm).
+For wflow\_sbm models there are two ways to include subsurface flow:
+
+1. The kinematic wave approach (see section [Subsurface flow
+   routing](../model_docs/lateral/kinwave.qmd#subsurface-flow-routing)) as part of the `sbm`
+   model type. Parameters that are part of this component are described in the [Lateral
+   subsurface flow](../model_docs/parameters_lateral.qmd#lateral-subsurface-flow) section of
+   Model parameters. Input parameters for this component are derived from the SBM vertical
+   concept and the land slope. One external parameter (`ksathorfrac`) is used to calculate the
+   horizontal hydraulic conductivity at the soil surface `kh_0`.
+2. Groundwater flow (see section [Groundwater flow component](../model_docs/lateral/gwf.qmd))
+   as part of the `sbm_gwf` model type. For the unconfined aquifer the input parameters are
+   described in the section [Unconfined
+   aquifer](../model_docs/parameters_lateral.qmd#unconfined-aquifer) of Model parameters. The
+   bottom (`bottom`) of the groundwater layer is derived from from the `soilthickness` [mm]
+   parameter of `SBM` and the provided surface elevation `altitude` [m] as part of the static
+   input. The `area` parameter is derived from the model grid. Parameters that are part of the
+   boundary conditions of the unconfined aquifer are listed under [Constant
+   Head](../model_docs/lateral/gwf.qmd#head-boundary) and [Boundary
+   conditions](../model_docs/parameters_lateral.qmd#boundary-conditions) of the Model
+   parameters section.
 
 Most hydrological model configurations make use of the kinematic wave surface routing (river
 flow, overland flow or both) and input data required for the river and overland flow components
-is described in [Surface flow](@ref).  There is also the option to use the local inertial model
-as part of the wflow\_sbm models (model types `sbm` and `sbm_gwf`):
-+ for river flow, see also the [Local inertial river and floodplain](@ref
-  config_sbm_gwf_lie_river) model.
-+ for 1D river flow and 2D overland flow combined, see also the [Local inertial river (1D)
-  and land (2D)](@ref config_sbm_gwf_lie_river_land) model.
-
-Input parameters for this approach are described in [River flow (local inertial)](@ref
-local-inertial_river_params), including the optional 1D [floodplain schematization](@ref
-local-inertial_floodplain_params), and [Overland flow (local inertial)](@ref
-local-inertial_land_params) of the Model parameters section.
+is described in [Surface flow](../model_docs/parameters_lateral.qmd#surface-flow). There is
+also the option to use the local inertial model as part of the wflow\_sbm models (model types
+`sbm` and `sbm_gwf`):
+
++ for river flow, see also the [Local inertial river and
+  floodplain](../model_docs/model_configurations.qmd#sbm-local-inertial-river) model.
++ for 1D river flow and 2D overland flow combined, see also the [Local inertial river (1D) and
+  land (2D)](../model_docs/model_configurations.qmd#sbm-local-inertial-river-1d-and-land-2d)
+  model.
+
+Input parameters for this approach are described in [River flow (local
+inertial)](../model_docs/parameters_lateral.qmd#local-inertial), including the optional 1D
+[floodplain schematization](../model_docs/parameters_lateral.qmd#d-floodplain), and [Overland
+flow (local inertial)](../model_docs/parameters_lateral.qmd#overland-flow) of the Model
+parameters section.
 
 Reservoirs or lakes can be part of the kinematic wave or local inertial model for river flow
-and input parameters are described in [Reservoirs](@ref reservoir_params) and [Lakes](@ref
-lake_params).
-
-The [wflow\_sediment](@ref config_sediment) model configuration consists of the vertical [Soil
-Erosion](@ref) concept and the input parameters for this concept are described in the
-[Sediment](@ref params_sediment) section of the Model parameters. The parameters of the lateral
-[Sediment Flux in overland flow](@ref) concept are described in the [Overland flow](@ref)
-section of the Model parameters. Parameters of this component are not directly set by data from
-static input. The input parameters of the lateral concept [River Sediment Model](@ref) are
-listed in [River flow](@ref) of the Model parameters section.
+and input parameters are described in
+[Reservoirs](../model_docs/parameters_lateral.qmd#reservoirs) and
+[Lakes](../model_docs/parameters_lateral.qmd#lakes).
+
+The [wflow\_sediment](../model_docs/model_configurations.qmd#wflow_sediment) model
+configuration consists of the vertical [Soil Erosion](../model_docs/vertical/sediment.qmd)
+concept and the input parameters for this concept are described in the
+[Sediment](../model_docs/parameters_vertical.qmd#sediment) section of the Model parameters. The
+parameters of the lateral [Sediment Flux in overland
+flow](../model_docs/lateral/sediment_flux.qmd#sediment-flux-in-overland-flow) concept are
+described in the [Overland flow](../model_docs/parameters_lateral.qmd#overland-flow-1) section
+of the Model parameters. Parameters of this component are not directly set by data from static
+input. The input parameters of the lateral concept [River Sediment
+Model](../model_docs/lateral/sediment_flux.qmd#river-sediment-model) are listed in [River
+flow](../model_docs/parameters_lateral.qmd#river-flow-1) of the Model parameters section.
 
 The Model parameters section lists all the parameters per Model component and these Tables can
 also be used to check which parameters can be part of the output, see also [Output netCDF
-section](@ref) and [Output CSV section](@ref).
+section](../user_guide/toml_file.qmd#output-netcdf-section) and [Output CSV
+section](../user_guide/toml_file.qmd#output-csv-section).
 
-Example models can be found in the [Example models section](@ref sample_data).
+Example models can be found in the [Example models section](./download_example_models.qmd).
 
 ## References
 + Yamazaki, D., Ikeshima, D., Sosa, J., Bates, P. D., Allen, G. H. and Pavelsky, T. M.: MERIT

docs/getting_started/download_example_models.qmd

@@ -14,8 +14,8 @@ listed in the Table below:
 
 The associated Model files (input static, forcing and state files) can easily be downloaded and
 for this we share the following Julia code (per Model) that downloads the required files to
-your current working directory. For running these test model see also [Usage](@ref run_wflow)
-and [Command Line Interface](@ref cli).
+your current working directory. For running these test model see also [Usage](./running_wflow.qmd#running-a-simulation)
+and [Command Line Interface](./running_wflow.qmd#using-the-command-line-interface).
 
 ## wflow\_sbm + kinematic wave
 ```julia

docs/getting_started/running_wflow.qmd

@@ -12,7 +12,7 @@ julia -e 'using Wflow; Wflow.run()' path/to/config.toml
 ```
 
 Furthermore, it is possible to write a Julia script to run a simulation. Example data to
-explore how this works can be found [here](@ref sample_data).
+explore how this works can be found [here](./download_example_models.qmd).
 
 ```julia
 using Wflow

docs/model_docs/index.qmd

@@ -8,8 +8,8 @@ modelling framework of wflow. Descriptions are given regarding the model concept
 the original scientific papers which explain the concepts in more detail. The model parameters
 which influence the processes are also shown, using inline code blocks. An overview of all
 model parameters is also provided for easy reference, including their short names, long
-descriptions and their units (see [parameters vertical concepts](@ref params_vert) and
-[parameters lateral concepts](@ref params_lat)).
+descriptions and their units (see [parameters vertical concepts](./parameters_vertical.qmd) and
+[parameters lateral concepts](./parameters_lateral.qmd)).
 
 ## Division between vertical and lateral
 

docs/model_docs/lateral/gwf.qmd

@@ -38,7 +38,7 @@ where $\SIb{S}{m m^{-1}}$ is storativity (or specific yield), $\SIb{\phi}{m}$ is
 head, $t$ is time, $\SIb{k}{m t^{-1}}$ is horizontal hydraulic conductivity, $\SIb{H}{m}$ is
 the (saturated) aquifer height: groundwater level - aquifer bottom elevation and $\SIb{Q}{m
 t^{-1}}$ represents fluxes from boundary conditions (e.g. recharge or abstraction), see also
-[Aquifer boundary conditions](@ref).
+[Aquifer boundary conditions](#aquifer-boundary-conditions).
 
 The simplest finite difference formulation is forward in time, central in space, and can be
 written as:
@@ -50,7 +50,7 @@ $$
 where $i$ is the cell index, $t$ is time, $\Delta t$ is the step size, $C_{i-1}$ is the the
 intercell conductance between cell $i-1$ and $i$ and $C_i$ is the intercell conductance between
 cell $i$ and $i+1$. The connection data between cells is stored as part of the `Connectivity`
-struct, see also [Connectivity](@ref) for more information.
+struct, see also [Connectivity](#connectivity) for more information.
 
 Conductance $C$ is defined as:
 
@@ -76,7 +76,7 @@ saturated thickness of a cell-to-cell is approximated using the cell with the hi
 This results in a consistent overestimation of the saturated thickness, but it avoids
 complexities related with cell drying and rewetting, such as having to define a "wetting
 threshold" or a "wetting factor". See also the documentation for MODFLOW-NWT (Niswonger et al.,
-2011) or MODFLOW6 (Langevin et al., 2017) for more background information. For more background
+1)    or MODFLOW6 (Langevin et al., 2017) for more background information. For more background
 on drying and rewetting, see for example McDonald et al. (1991).
 
 For the finite difference formulation, there is only one unknown, $\phi_i^{t+1}$. Reshuffling
@@ -164,9 +164,9 @@ the river bed exfiltration conductance, $\SIb{\subtext{B}{riv}}{L}$ the bottom o
 bed, $\SIb{\subtext{h}{riv}}{L}$ is the river stage and $\SIb{\phi}{L}$ is the hydraulic head
 in the river cell.
 
-The Table in the Groundwater flow [river boundary condition](@ref gwf_river_params) section of
-the Model parameters provides the parameters of the struct `River`. Parameters that can be set
-directly from the static input data (netCDF) are marked in this Table.
+The Table in the Groundwater flow [river boundary condition](../parameters_lateral.qmd#river)
+section of the Model parameters provides the parameters of the struct `River`. Parameters that
+can be set directly from the static input data (netCDF) are marked in this Table.
 
 The exchange flux (river to aquifer) $\subtext{Q}{riv}$ is an output variable (field `flux` of
 the `River` struct), and is used to update the total flux in a river cell. For the model `SBM +
@@ -184,9 +184,10 @@ where $\SIb{\subtext{Q}{drain}}{L^3 T^{-1}}$ is the exchange flux from drains to
 $\SIb{\subtext{C}{drain}}{L^2 T^{-1}}$ is the drain conductance, $\SIb{\subtext{h}{drain}}{L}$
 is the drain elevation and $\SIb{\phi}{L}$ is the hydraulic head in the cell with drainage.
 
-The table in the Groundwater flow [drainage boundary condition](@ref gwf_drainage_params)
-section of the Model parameters provides the parameters of the struct `Drainage`. Parameters
-that can be set directly from the static input data (netCDF) are marked in this Table.
+The table in the Groundwater flow [drainage boundary
+condition](../parameters_lateral.qmd#drainage) section of the Model parameters provides the
+parameters of the struct `Drainage`. Parameters that can be set directly from the static input
+data (netCDF) are marked in this Table.
 
 The exchange flux (drains to aquifer) $\subtext{Q}{drain}$ is an output variable (field `flux`
 of struct `Drainage`), and is used to update the total flux in a cell with drains. For the
@@ -208,10 +209,10 @@ $$
 
 with $\SIb{}{L T^{-1}}$ the recharge rate and $\SIb{A}{L^2}$ the area of the aquifer cell.
 
-The table in the Groundwater flow [recharge boundary condition](@ref gwf_recharge_params)
-section of the Model parameters section provides the parameters of the struct `Recharge`.
-Parameters that can be set directly from the static input data (netCDF) are marked in this
-Table.
+The table in the Groundwater flow [recharge boundary
+condition](../parameters_lateral.qmd#recharge) section of the Model parameters section provides
+the parameters of the struct `Recharge`. Parameters that can be set directly from the static
+input data (netCDF) are marked in this Table.
 
 The recharge flux $Q_r$ is an output variable (field `flux` of struct `Recharge`), and is used
 to update the total flux in a cell where recharge occurs. For the model `SBM + Groundwater
@@ -232,8 +233,9 @@ $$
 with $\SIb{C_{hb}}{L^2 T^{-1}}$ the conductance of the head boundary, $\SIb{\phi_{hb}}{L}$ the
 head of the head boundary and $\phi$ the head of the aquifer cell.
 
-The table in the Groundwater flow [head boundary condition](@ref gwf_headboundary_params)
-section of the Model parameters provides the parameters of the struct `HeadBoundary`.
+The table in the Groundwater flow [head boundary
+condition](../parameters_lateral.qmd#head-boundary) section of the Model parameters provides
+the parameters of the struct `HeadBoundary`.
 
 The head boundary flux $Q_{hb}$ is an output variable (field `flux` of struct `HeadBoundary`),
 and is used to update the total flux in a cell where this type of boundary occurs. The
@@ -246,8 +248,8 @@ This boundary is not (yet) part of the model `SBM + Groundwater flow`.
 ### Well boundary
 A volumetric well rate $\SIb{}{L^3 T^{-1}}$ can be specified as a boundary condition.
 
-The Table in the [well boundary condition](@ref well_boundary_params) section of the Model
-parameters provides the parameters of the struct `Well`.
+The Table in the [well boundary condition](../parameters_lateral.qmd#well-boundary) section of
+the Model parameters provides the parameters of the struct `Well`.
 
 The volumetric well rate $\subtext{Q}{well}$ can be can be specified as a fixed or time
 dependent value. If a cell is dry, the actual well flux `flux` is set to zero (see also the