diff --git a/hugo/content/ex/fit/bayesian.md b/hugo/content/ex/fit/bayesian.md
index 3af0544662071032ba0b15289f68281522b3a004..d0802b67c88d509f122b5ffea8249ee783be8b10 100644
--- a/hugo/content/ex/fit/bayesian.md
+++ b/hugo/content/ex/fit/bayesian.md
@@ -7,7 +7,7 @@ weight = 40
 
 Bayesian sampling of reflectometry models is a common tool in the analysis of specular reflectometry data.
 The Python programming language has a powerful infrastructure for this modelling, including packages such as [PyMC3](https://docs.pymc.io) and [PyStan](https://pystan.readthedocs.io/en/latest/).
-Here, we will show how the [emcee](https://emcee.readthedocs.io/en/stable/) Python may be used to enable Bayesian sampling in BornAgain and the differential evoulation optimisation algorithm from the [scipy](https://www.scipy.org/scipylib/index.html).
+Here, we will show how the [emcee](https://emcee.readthedocs.io/en/stable/) Python may be used to enable Bayesian sampling in BornAgain and the differential evoulation optimisation algorithm from the [scipy](https://docs.scipy.org/doc/scipy/).
 
 ### Example script
 
@@ -16,7 +16,9 @@ To generate these images of the probability distributions of the parameters and
 {{< figscg src="/files/fitted/CornerPlotBayes.png" width="500" class="center">}}
 {{< figscg src="/files/fitted/ReflectivityBayes.png" width="500" class="center">}}
 
-run [this script]({{% ref-ex "bayesian/likelihood_sampling.py" %}}).
+run this script
+
+{{< show-ex file="bayesian/likelihood_sampling.py" >}}
 
 
 ### Explanation
@@ -27,7 +29,7 @@ We know the scattering length densities for each, and that in total there are 10
 This sample is created in the `get_sample` function.
 
 Having built the sample, it is necessary to obtain the real experimental data.
-For the above code to work locally, the following [data file]({{% ref-ex "data/genx_interchanging_layers.dat.gz?inline=false" %}}) is required and the Python script (in particular the `get_real_data` function) should be adapted appropriately.
+For the above code to work locally, the data file {{% ref-data genx_alternating_layers.dat.gz %}} is required and the Python script (in particular the `get_real_data` function) should be adapted appropriately.
 This function defined an uncertainty in the reflectivity of 10 %.
 
 The simulation is then defined in the `get_simulation` function, which is passed a series of angles, however, this may be modified to perform a Q-scan as necessary.
diff --git a/hugo/content/ex/fit/external-minimizer-with-plotting.md b/hugo/content/ex/fit/external-minimizer-with-plotting.md
index 0f607cba70ec75a4c3313551cb91735810ea35a5..27a74568eb615a6a32ecc897477a8f237e74c209 100644
--- a/hugo/content/ex/fit/external-minimizer-with-plotting.md
+++ b/hugo/content/ex/fit/external-minimizer-with-plotting.md
@@ -5,7 +5,7 @@ weight = 40
 
 ## External Minimizers: Plotting Fit Progress
 
-In this example we are demonstrating how to run a typical fitting task in BornAgain using a third party minimizer while plotting the results. As in our [previous example](/ex/fit/extended/external-minimizer), we use lmfit for sake of illustration.
+In this example we are demonstrating how to run a typical fitting task in BornAgain using a third party minimizer while plotting the results. As in our [previous example](/ex/fit/external-minimizer), we use lmfit for sake of illustration.
 
 To plot the fit progress, it is needed to use the lmfit iteration callback function. It will come handy to define the plotting callback function as a specialized class:
 
diff --git a/hugo/content/ex/fit/fit-with-uncertainties.md b/hugo/content/ex/fit/fit-with-uncertainties.md
index f173d1ca697fe88ab4d343c44c85afd7651c81ba..fceb6742892d52d409fe9b0ad87c7600a68dd2f6 100644
--- a/hugo/content/ex/fit/fit-with-uncertainties.md
+++ b/hugo/content/ex/fit/fit-with-uncertainties.md
@@ -10,7 +10,7 @@ In this example we are demonstrating how to allow for uncertainties during a Ref
 
 The reference data was generated with GENX, setting the thickness of the Ti layers equal to 3 nm.
 
-This example follows closely the tutorial on [Fitting reflectometry data](/ex/fit/extended/fit-specular-data/). The main points to focus on here are the following:
+The main points to focus on here are the following:
 
  - Added artificial uncertainties to the data being fitted
  - Use of the the $RQ^4$ view for plotting
diff --git a/hugo/content/ex/fit/galaxi.md b/hugo/content/ex/fit/galaxi.md
index b300fb07b8adb1d219e6702261a932b94981dd9b..5e8553e5d51e226fd68d04bd22827dacde89052b 100644
--- a/hugo/content/ex/fit/galaxi.md
+++ b/hugo/content/ex/fit/galaxi.md
@@ -5,7 +5,7 @@ weight = 30
 
 ## Experiment at GALAXI
 
-This is an example of a real data fit. We use our own measurements performed at the laboratory diffractometer [GALAXI](http://www.fz-juelich.de/jcns/jcns-2//DE/Leistungen/GALAXI/_node.html) in Forschungszentrum Jülich.
+This is an example of a real data fit. We use our own measurements performed at the laboratory diffractometer [GALAXI](https://www.fz-juelich.de/en/jcns/jcns-2/expertise/in-house-x-ray/galaxi) in Forschungszentrum Jülich.
 
 {{< galleryscg >}}
 {{< figscg src="/img/draw/FitGALAXIData_setup.jpg" width="350px" caption="Real-space model">}}
@@ -20,8 +20,6 @@ This is an example of a real data fit. We use our own measurements performed at
 * The real data is loaded from a tiff file into a histogram representing the detector's channels.
 * The `run_fitting()` function contains the initialization of the fitting kernel: loading experimental data, assignment of fit pair, fit parameters selection (line 62).
 
-{{< show-ex file="fit/scatter2d/expfit_galaxi.py" >}}
-
 ## Experiment description
 
 To successfully simulate and fit results of some real experiment it is important to have
@@ -32,10 +30,7 @@ To successfully simulate and fit results of some real experiment it is important
 
 ### Experiment
 
-As an example we will use our own measurements performed  at the laboratory diffractometer [GALAXI](http://www.fz-juelich.de/jcns/jcns-2//DE/Leistungen/GALAXI/_node.html) in Forschungszentrum Jülich.
-
-A complete example, containing less explanations but more code, can be found in
-[Real life fit example: experiment at GALAXI](/ex/fit/extended/experiment-at-galaxi).
+As an example we will use our own measurements performed  at the laboratory diffractometer [GALAXI](https://www.fz-juelich.de/en/jcns/jcns-2/expertise/in-house-x-ray/galaxi) in Forschungszentrum Jülich.
 
 Our sample represents a 3-layer system (substrate, teflon and air)
 with Ag nanoparticles sitting on top of the teflon layer.
@@ -125,3 +120,7 @@ data = img.data.astype("float64")
 ```
 
 The main requirement is that the shape of the numpy array coincides with the number of detector channels (i.e. `npx, npy = 981, 1043` for given example).
+
+{{< show-ex file="fit/scatter2d/expfit_galaxi.py" >}}
+
+Data to be fitted: {{% ref-data galaxi_data.tif.gz %}}
diff --git a/hugo/content/ex/fit/gisas-fit2d.md b/hugo/content/ex/fit/gisas-fit2d.md
index c2fdcd44a637205b5edac1bffef5ccd87d77cb10..0b31b62ad2ebf7fee6848effce7a0d8c82c2f803 100644
--- a/hugo/content/ex/fit/gisas-fit2d.md
+++ b/hugo/content/ex/fit/gisas-fit2d.md
@@ -26,8 +26,7 @@ to make the subsequent fitting more difficult and more realistic:
   * Beam wavelength and alpha_i slightly changed;
   * Detector x-axis skewed.
 
-The faked data can be found at
-{{% ref-ex "data/faked-gisas1.txt.gz" %}}.
+The faked data: {{% ref-data faked-gisas1.txt.gz %}}
 
 ## Fit script
 
diff --git a/hugo/content/ex/fit/minimizer-settings.md b/hugo/content/ex/fit/minimizer-settings.md
index 2e0a2f72d8f09193478544b65625c7ff8bb5b372..57bfa0ee39bd81f833eaa93f98b74b421e48761d 100644
--- a/hugo/content/ex/fit/minimizer-settings.md
+++ b/hugo/content/ex/fit/minimizer-settings.md
@@ -22,6 +22,6 @@ print(ba.MinimizerFactory().catalogueDetailsToString())
 
 
 For more information, see the
-[minimizer settings tutorial](/ex/fit/minimizers/index.md).
+[minimizer settings tutorial](/ref/fit/minimizers).
 
 {{< show-ex file="fit/scatter2d/minimizer_settings.py" >}}
diff --git a/hugo/content/ex/fit/polarized-spinasymmetry-fit.md b/hugo/content/ex/fit/polarized-spinasymmetry-fit.md
index 39117f36e55c7f2c51d1d867a95f9658f81c2fe7..17ef2b0e0be84f58774e05db442703b44dbcef9d 100644
--- a/hugo/content/ex/fit/polarized-spinasymmetry-fit.md
+++ b/hugo/content/ex/fit/polarized-spinasymmetry-fit.md
@@ -41,7 +41,7 @@ If no uncertainties are available, using the relative difference `fit_objective.
 If the relative difference is selected and uncertainties are provided, BornAgain automatically falls back to the above $\chi^2$ metric.
 
 The fitting of polarized reflectometry data proceeds similar to the lines presented in
-[the tutorial on multiple datasets](/ex/fit/advanced/multiple-datasets).
+[the tutorial on multiple datasets](/ex/fit/multiple-datasets).
 We need to add the reflectivity curves for the up-up and down-down channel
 to the fit objective:
 
@@ -98,3 +98,5 @@ python3 PolarizedSpinAsymmetryFit.py
 Here is the complete example:
 
 {{< show-ex file="fit/specular/PolarizedSpinAsymmetryFit.py" >}}
+
+Data to be fitted: {{% ref-data MAFO_Saturated_mm.tab %}}, {{% ref-data MAFO_Saturated_pp.tab %}}
diff --git a/hugo/content/ex/fit/reflectometry-honeycomb.md b/hugo/content/ex/fit/reflectometry-honeycomb.md
index 438609f895cc438b9b918bda9d7305d6e76a8e26..52402554587059635b0212f588c5a5e67fbc3acc 100644
--- a/hugo/content/ex/fit/reflectometry-honeycomb.md
+++ b/hugo/content/ex/fit/reflectometry-honeycomb.md
@@ -33,7 +33,7 @@ magnetizations at 150K and 300K: $M_{s150} = M_{150K} / M_{300K}$.
 #### Magnetization model
 
 To model a magnetic material, one can assign a magnetization vector to any material, as is demonstrated
-in the [basic polarized reflectometry tutorial](/ref/instr/pol/basic-polarized-reflectometry).
+in the [magnetic material tutorial](/ref/sample/material/magnetization).
 When a non-vanishing magnetization vector is specified for at least one layer in a sample,
 BornAgain will automatically utilize the polarized computational engine.
 This leads to lower performance as the computations are more invovled.
@@ -148,4 +148,4 @@ As can be seen from the plot of the SLDs, the magnetization is indeed larger for
 
 {{< show-ex file="fit/specular/Honeycomb_fit.py" >}}
 
-Reference data: {{% ref-ex "data/honeycomb" %}}
+Data to be fitted: {{% ref-data honeycomb150m.dat %}}, {{% ref-data honeycomb150p.dat %}}, {{% ref-data honeycomb300m.dat %}}, {{% ref-data honeycomb300p.dat %}}
diff --git a/hugo/content/ex/fit/reflectometry-pt-layer.md b/hugo/content/ex/fit/reflectometry-pt-layer.md
index 263d80df8442d32a2e18eca018b9d6ae7cf13704..039794fd08575f13bf18fe2a8ac2ff86d4001343 100644
--- a/hugo/content/ex/fit/reflectometry-pt-layer.md
+++ b/hugo/content/ex/fit/reflectometry-pt-layer.md
@@ -97,7 +97,6 @@ python3 Pt_layer_fit.py
 ```
 a simulation is performed with our fit results and one should obtain the result shown above.
 
-
 {{< show-ex file="fit/specular/Pt_layer_fit.py" >}}
 
-Data to be fitted: {{% ref-ex "data/RvsQ_36563_36662.txt.gz" %}}
+Data to be fitted: {{% ref-data RvsQ_36563_36662.txt.gz %}}
diff --git a/hugo/content/ex/result/export/_index.md b/hugo/content/ex/result/export/_index.md
index fe8dfcaf0dc13ff4b9b7030f606c21e26b9c74ff..21cc68ff7792aeb96167b11ffe770ec07ca44177 100644
--- a/hugo/content/ex/result/export/_index.md
+++ b/hugo/content/ex/result/export/_index.md
@@ -82,6 +82,3 @@ hist.save("result.int.gz")
 Additional information can be found in the following pages:
 
 * [Plotting with axes in different units](/ex/result/export/axes-in-different-units)
-* [SimulationResult C++ class reference](http://apps.jcns.fz-juelich.de/doxy/BornAgain/classSimulationResult.html)
-* [Histogram1D C++ class reference](http://apps.jcns.fz-juelich.de/doxy/BornAgain/classHistogram1D.html)
-* [Histogram2D C++ class reference](http://apps.jcns.fz-juelich.de/doxy/BornAgain/classHistogram2D.html)
diff --git a/hugo/content/ex/result/export/axes-in-different-units/index.md b/hugo/content/ex/result/export/axes-in-different-units/index.md
index 6773d4eaa3d303afa6d828572ab3ef7a88543e5b..442423ad7fb49a535269d05e1d867fd898df6445 100644
--- a/hugo/content/ex/result/export/axes-in-different-units/index.md
+++ b/hugo/content/ex/result/export/axes-in-different-units/index.md
@@ -6,7 +6,7 @@ weight = 20
 ### Plotting with axes in different units
 
 In this example we demonstrate how to plot intensity data with detector axes expressed in different units. It serves as a supporting example to the
-[Accessing simulation results](/py/export/_index.md) tutorial.
+[Accessing simulation results](/ex/result/export/more) tutorial.
 
 * The standard [Cylinders in DWBA](/ex/sim/gisas)
 sample is used to setup the simulation.
diff --git a/hugo/content/ex/sample/roughness/specular_2models.md b/hugo/content/ex/sample/roughness/specular_2models.md
index 3067152b176c1dcc12c6b3a9b8489ce947f8999b..e20cc998cee7861a5627c72ef1242504fb760a95 100644
--- a/hugo/content/ex/sample/roughness/specular_2models.md
+++ b/hugo/content/ex/sample/roughness/specular_2models.md
@@ -8,8 +8,8 @@ weight = 15
 This example demonstrates how to apply different roughness models
 in a specular reflectivity calculation. The considered sample is
 exactly the same as the one described in the
-[reflectometry tutorial](/ref/sim/class/specular/_index.md),
-and the [basic roughness tutorial](/ref/sample/roughness/specular).
+[reflectometry tutorial](/ref/sim/class/specular),
+and the [basic roughness tutorial](/ref/sample/roughness).
 Hewever, now the computation is performed twice with the standard $tanh$ interface profile
 and the Névot-Croce roughness model that arises from a Gaussian distribution of the
 deviation from the mean-surface position.
diff --git a/hugo/content/ex/sample/roughness/specular_default.md b/hugo/content/ex/sample/roughness/specular_default.md
index f168aaafeb2655f06fa40552ebeb25a414231ea4..faeb5b7d3c1190c9cb480e96051cd0c957b98b8d 100644
--- a/hugo/content/ex/sample/roughness/specular_default.md
+++ b/hugo/content/ex/sample/roughness/specular_default.md
@@ -8,7 +8,7 @@ weight = 10
 This example demonstrates how to compute reflected signal from
 a multilayered sample with surface roughness. All the experiment
 layout is exactly the same as the one described in
-[reflectometry tutorial](/ref/sim/class/specular/_index.md),
+[reflectometry tutorial](/ref/sim/class/specular),
 but now all the layers (except the ambient media) have roughness on the top surface. The
 roughness is characterized by root-mean-square deviation from the mean surface position
 $\sigma = 1$ nm.
@@ -16,7 +16,7 @@ $\sigma = 1$ nm.
 {{<figscg src="/img/auto/specular/SpecularSimulationWithRoughness.png" width="350px">}}
 
 When comparing the result of the simulation to the result obtained in the
-[reflectometry tutorial](/ref/sim/class/specular/_index.md),
+[reflectometry tutorial](/ref/sim/class/specular),
 one can notice up to two orders of magnitude attenuation of the reflected signal due to
 the roughness of the sample.
 
diff --git a/hugo/content/ex/sim/specular.md b/hugo/content/ex/sim/specular.md
index aabb1fb6d42e2a43c065f2f780caf2accd06c172..10dd940feda8870881b416d5abcf2efafa06f182 100644
--- a/hugo/content/ex/sim/specular.md
+++ b/hugo/content/ex/sim/specular.md
@@ -10,8 +10,8 @@ by a sample that consists of 10 Ti/Ni double layers on a Si substrate.
 
 ##### Full script
 
-The same script has been used in the tutorial to explain [usage](/py/run.md)
-and [syntax](/py/syntax.md) of BornAgain Python code.
+The same script has been used in the tutorial to explain [usage](/py/run)
+and [syntax](/py/syntax) of BornAgain Python code.
 
 Root class reference: [SpecularSimulation](/ref/sim/class/specular).
 
diff --git a/hugo/content/installation/py/linux.md b/hugo/content/installation/py/linux.md
index e1d6223425aee86d54795aa4b4835ef41a16b939..6473349dd06a5ed7045cc0e826ee1dd87f3a84d4 100644
--- a/hugo/content/installation/py/linux.md
+++ b/hugo/content/installation/py/linux.md
@@ -14,9 +14,13 @@ some point (e.g. Debian 12) disabled Pip, which terminates with
 `error: externally-managed-environment`. While this behavior can be
 overridden by a special flag, we advise against.
 
+#### Python in pyenv
+
 Rather, we recommend escaping from Python version hell by using the
 Python version manager [pyenv](https://github.com/pyenv/pyenv).
 
+Install the venerable GUI toolkit Tk (e.g. Debian package tk-dev).
+
 Prepare the shell by adding
 ```
 export PYENV_ROOT="$HOME/.pyenv"
@@ -40,4 +44,4 @@ which python # shows path in virtual environment
 pip install numpy
 ```
 etc.
-For the full list of modules required by BornAgain, see the [modules](modules) page.
+For the full list of modules required by BornAgain, see the [modules](/installation/py/modules/) page.
diff --git a/hugo/content/installation/py/modules.md b/hugo/content/installation/py/modules.md
index e6a3af3598f95ee4b80d66867a7bed304539d770..22c9bbbb3f964ea1f348f89066b0b646b6ea78d1 100644
--- a/hugo/content/installation/py/modules.md
+++ b/hugo/content/installation/py/modules.md
@@ -19,6 +19,7 @@ Furthermore, a small number of fit script examples require the Python modules
   * lmfit
   * scipy
   * tqdm
+
 These are not required for _installing_ and _running_ most of BornAgain.
 However, they should be present when _building_ BornAgain
 lest some tests will fail.
diff --git a/hugo/content/ref/fit/minimizers.md b/hugo/content/ref/fit/minimizers.md
index 1b78fa04722cef2bef2238aba3c3d0dab4dd3a7e..c8356fa62fad9497c5fdd72bcfacf0b251997870 100644
--- a/hugo/content/ref/fit/minimizers.md
+++ b/hugo/content/ref/fit/minimizers.md
@@ -190,4 +190,4 @@ BornAgain fitting can also be done using other minimization packages. A short li
 + [lmfit](https://lmfit.github.io/lmfit-py/)
 + [bumps](https://bumps.readthedocs.io/en/latest/)
 
-In [this example](/ex/fit/extended/external-minimizer) we demonstrate how to use the `lmfit` minimizer for a typical fit of GISAS data.
+In [this example](/ex/fit/external-minimizer) we demonstrate how to use the `lmfit` minimizer for a typical fit of GISAS data.
diff --git a/hugo/content/ref/instr/beam/_index.md b/hugo/content/ref/instr/beam/_index.md
index a840584861169831d0b7fc9cb27d4bc4cca38aac..09050fda2e83a601feafc671f5e1abbb17f2cd03 100644
--- a/hugo/content/ref/instr/beam/_index.md
+++ b/hugo/content/ref/instr/beam/_index.md
@@ -24,7 +24,7 @@ After creation of a beam, special properties can be set with
 beam.setFootprintFactor(footprint)
 beam.setPolarization(polarization)
 ```
-For the arguments, see [footprint](footprint) and [polarization](../polarized).
+For the arguments, see [footprint](footprint) and [polarization](../pol).
 
 
 {{% children  %}}
diff --git a/hugo/content/ref/instr/beam/angular-divergence/index.md b/hugo/content/ref/instr/beam/angular-divergence/index.md
index 2b1413c3ce2f5cc1fbbe769f3ce830c2d8cd287c..8d13a5079a0d64fee8b1d69f3c3b51093f3524e2 100644
--- a/hugo/content/ref/instr/beam/angular-divergence/index.md
+++ b/hugo/content/ref/instr/beam/angular-divergence/index.md
@@ -8,7 +8,7 @@ weight = 60
 This example demonstrates beam angular spread effects in reflectivity computations.
 It also offers a comparison with data generated using another well known code: GenX.
 Further information about reflectometry simulations can be found in the
-[Reflectometry Simulation Tutorial](/ref/sim/class/specular/_index.md).
+[Reflectometry Simulation Tutorial](/ref/sim/class/specular).
 
 The observed reflectometry signal can be affected either by a spread in the beam wavelength or in the incident angle.
 
diff --git a/hugo/content/ref/instr/beam/footprint/index.md b/hugo/content/ref/instr/beam/footprint/index.md
index 0c1dc5167506b70d1875d1d0239efb72bfcf62b4..44540c43a46e9ce224ec71f1ac2805efe2d0d0f0 100644
--- a/hugo/content/ref/instr/beam/footprint/index.md
+++ b/hugo/content/ref/instr/beam/footprint/index.md
@@ -47,7 +47,7 @@ The incident angle range was made rather small in this example
 (from $0.0$ to $0.6$ degrees) in order to emphasize
 the footprint impact at small incident angles.
 In other respects this example exactly matches the
-[reflectometry simulation tutorial](/ref/sim/class/specular/_index.md).
+[reflectometry simulation tutorial](/ref/sim/class/specular).
 
 {{< galleryscg >}}
 {{< figscg src="/img/auto/specular/FootprintCorrection.png" width="450px">}}
diff --git a/hugo/content/ref/instr/beam/full-divergence/index.md b/hugo/content/ref/instr/beam/full-divergence/index.md
index 6ec8568dff038707d7aeb22426dfa4f5280cc825..7a9ca8ca8c13fe4c4b9038c693fc15996ee7f33e 100644
--- a/hugo/content/ref/instr/beam/full-divergence/index.md
+++ b/hugo/content/ref/instr/beam/full-divergence/index.md
@@ -8,7 +8,7 @@ weight = 65
 This example demonstrates beam wavelength spread effects in reflectivity computations.
 All simulation parameters (except for those related to beam spread itself)
 coincide with those defined in
-[reflectometry simulation tutorial](/ref/sim/class/specular/_index.md).
+[reflectometry simulation tutorial](/ref/sim/class/specular).
 
 In real specular experiments the observed reflectivity is always affected
 by the beam spread in both wavelength and incident angle.
diff --git a/hugo/content/ref/instr/det/_index.md b/hugo/content/ref/instr/det/_index.md
index b1d9c37a24a6a155ec0cfc1083833a644a0a3077..1080a50646f706bc80ce9abef12bb5b28927bd95 100644
--- a/hugo/content/ref/instr/det/_index.md
+++ b/hugo/content/ref/instr/det/_index.md
@@ -26,10 +26,10 @@ When fitting theoretical models to measured diffraction images,
 it can be helpful to mask part of the detector area.
 See
 
-* [Fit with masks](/ex/fit/advanced/fit-with-masks)
+* [Fit with masks](/ex/fit/fit-with-masks)
 
 ### Resolution
 
 For modeling the detector resolution, see
 
-* [Detector resolution example](/ref/instr/det/resolution)
+* [Detector resolution manual](/ref/instr/det/resolution)
diff --git a/hugo/content/ref/instr/pol/_index.md b/hugo/content/ref/instr/pol/_index.md
index ac894bd99ce909a1a67bfa22d0033fa1be7399a5..695651789a657e8ee763eb7d50b0d5cf09bb9bc3 100644
--- a/hugo/content/ref/instr/pol/_index.md
+++ b/hugo/content/ref/instr/pol/_index.md
@@ -10,7 +10,7 @@ if there is magnetism in the sample model
 or if a polarizer is set in the instrument model.
 
 Sample magnetization is explained in
-[Sample model > Materials > Magnetization](ref/sample/material/magnetization).
+[Sample model > Materials > Magnetization](/ref/sample/material/magnetization).
 
 Beam polarization is set through
 ```python
diff --git a/hugo/content/ref/instr/pol/polarized-spinasymmetry/index.md b/hugo/content/ref/instr/pol/polarized-spinasymmetry/index.md
index 12e58fd9af7856eeb3d2aacc8f31ad8638bd4c20..44d799ce34cffdc6691de66ebdefc187bb9af35d 100644
--- a/hugo/content/ref/instr/pol/polarized-spinasymmetry/index.md
+++ b/hugo/content/ref/instr/pol/polarized-spinasymmetry/index.md
@@ -15,7 +15,7 @@ During these tutorials, we neglect the magnetically dead layer that forms below
 
 In this first example, we utilize parameters that are deduced from a fit to the data provided on the NIST homepage.
 How to perform the fit is described in the
-[extended example](/ex/fit/extended/polarized-spinasymmetry-fit).
+[extended example](/ex/fit/polarized-spinasymmetry-fit).
 
 
 
diff --git a/hugo/content/ref/other/distributions.md b/hugo/content/ref/other/distributions.md
index 70ee4afefdb7da8771bbe4e0481a72df3d2e746f..f3a69a2273980867da7603c0c37c5aec86b7ed18 100644
--- a/hugo/content/ref/other/distributions.md
+++ b/hugo/content/ref/other/distributions.md
@@ -29,7 +29,7 @@ parsamples = distr.distributionSamples()
 returns a vector of parameter samples. Each `ParameterSample` has a `value` and a `weight`.
 The sample (scattering target) model is then constructed as incoherent sum of components
 with given parameter values and weights.
-For instance, in the [PolydisperseCylinders example](/ex/scatter2d/polydisperse-cylinders),
+For instance, in the [PolydisperseCylinders example](/ex/sample/particles/polydispersity),
 a layout is filled with uncorrelated particles:
 ```python
 distr = ba.DistributionGaussian(10*nm, 1*nm)
@@ -41,5 +41,5 @@ for parsample in distr.distributionSamples():
 
 ##### Examples
 
-- [PolydisperseCylinders](/ex/sample/polydispersity): layout filled with uncorrelated particles
-- [LatticeOrientationDistribution](/ex/sample/lattice-ori-distr): layer filled with uncorrelated layouts
\ No newline at end of file
+- [PolydisperseCylinders](/ex/sample/particles/polydispersity): layout filled with uncorrelated particles
+- [LatticeOrientationDistribution](/ex/sample/assemblies/lattice-ori-distr): layer filled with uncorrelated layouts
diff --git a/hugo/content/ref/other/rotation.md b/hugo/content/ref/other/rotation.md
index 3ac1a273e83fa709ba14e7fa8a5bf8f6e630883a..0fdd96773cfc0b495b19b654c75807d0fb46e657 100644
--- a/hugo/content/ref/other/rotation.md
+++ b/hugo/content/ref/other/rotation.md
@@ -52,4 +52,4 @@ the original coordinate system.
 
 ##### Examples
 
-- [particle rotation](/ex/sample/particle-rotation)
\ No newline at end of file
+- [particle rotation](/ex/sample/particles/particle-rotation)
diff --git a/hugo/content/ref/sample/material/magnetization.md b/hugo/content/ref/sample/material/magnetization.md
index dcfed75d7efebb00019b282517c6fd37b4eb0f08..c098064cd098f046856ba7c38b7c99718c3ff73b 100644
--- a/hugo/content/ref/sample/material/magnetization.md
+++ b/hugo/content/ref/sample/material/magnetization.md
@@ -19,4 +19,4 @@ material = ba.RefractiveMaterial(name, delta, beta, magnetic_field)
 material = ba.MaterialBySLD(name, sld_real, sld_imag, magnetic_field)
 ```
 
-Examples are under [Examples > Instrument > Neutron polarization](ex/instr/pol).
+Examples are under [Examples > Instrument > Neutron polarization](/ex/instr/pol).
diff --git a/hugo/content/ref/sample/multilayer/_index.md b/hugo/content/ref/sample/multilayer/_index.md
index 8ed6000317ef3e6aca4c001375428b33c401c191..594eab1d62af8342ff3cc9806fafc6cff85f0af7 100644
--- a/hugo/content/ref/sample/multilayer/_index.md
+++ b/hugo/content/ref/sample/multilayer/_index.md
@@ -33,7 +33,7 @@ Global properties of the sample are set through the following functions:
 ```python
 sample.setRoughnessModel(roughnessModel)
 ```
-which takes an argument of type [RoughnessModel](/ref/sample/roughness/profiles);
+which takes an argument of type [RoughnessModel](/ex/sample/roughness/specular_2models);
 
 ```python
 sample.setCrossCorrLength(crossCorrLength)
diff --git a/hugo/content/ref/sample/particle/_index.md b/hugo/content/ref/sample/particle/_index.md
index 744ce5320aff7f6dc299b2695e4e7fe3ecb73f5a..eb2097083027c0c61b9c5b3047ef8950c86285fd 100644
--- a/hugo/content/ref/sample/particle/_index.md
+++ b/hugo/content/ref/sample/particle/_index.md
@@ -45,11 +45,11 @@ For the constructor arguments, see sections [Material](/ref/sample/material)
 and [Formfactor](/ref/sample/particle/ff).
 
 To create a composed particle, see
-- [CoreShellParticle](/sample/particle/composition/core-shell),
-- [Compound](/sample/particle/composition) - also used as base in lattices,
+- [CoreShellParticle](/ref/sample/particle/composition/core-shell),
+- [Compound](/ref/sample/particle/composition/compound) - also used as base in lattices,
 - Mesocrystal.
 
-[Magnetization](/ref/sample/particle/magnetic) is supported as a material property.
+[Magnetization](/ref/sample/material/magnetization) is supported as a material property.
 
 ##### Set location and orientation
 
diff --git a/hugo/content/ref/sample/particle/composition/core-shell.md b/hugo/content/ref/sample/particle/composition/core-shell.md
index 862cf10192095b8074cc782e06b87c3e50962b7a..8d58f43f329b5a067a45fd4fb61229ed1e7d962d 100644
--- a/hugo/content/ref/sample/particle/composition/core-shell.md
+++ b/hugo/content/ref/sample/particle/composition/core-shell.md
@@ -30,6 +30,6 @@ opposite argument order, namely `(shell, core)`.
 
 ##### Example
 
-See [Core-and-shell example](/ex/sample/core-shell-particle).
+See [Core-and-shell example](/ex/sample/particles/core-shell-particle).
 Validated through an alternative implementation that uses particle composition,
 {{% ref-ex "scatter2d/CoreShellNanoparticles2.py" %}}.
diff --git a/hugo/content/ref/sample/particle/ff/_index.md b/hugo/content/ref/sample/particle/ff/_index.md
index 6e192c9c8f29f9f3de69c9cf1083790a43918d31..4eaafdf64383942f840c43b47f00b854c2b0d25a 100644
--- a/hugo/content/ref/sample/particle/ff/_index.md
+++ b/hugo/content/ref/sample/particle/ff/_index.md
@@ -21,7 +21,7 @@ to the outside limit of&nbsp;0.
 At large $q$, the exponential factor in the integral defining $F(\mathbf{q})$
 oscillates rapidly. This leads to substantial errors if $q$ is of the same order
 or larger than the inverse detector bin length.
-In such cases, we recommend [Monte-Carlo integration over detector bins](/py/sim/option/mc).
+In such cases, we recommend [Monte-Carlo integration over detector bins](/ref/sim/setup/options/mc).
 
 By construction, $F(\mathbf{q})$ is a holomorphic function.
 Therefore expressions previously derived for real wave vectors $\mathbf{q}$
@@ -29,7 +29,7 @@ also hold for complex $\mathbf{q}$.
 
 #### Implementation
 
-The interface class [IFormFactor]({{% ref-src "Sample/Particle/IFormFactor.h" %}})
+The interface class {{% ref-class "Sample/Particle" "IFormFactor" %}}
 cannot be instantiated directly.
 Instead, one has to choose one of the following child classes:
 
@@ -40,7 +40,7 @@ Instead, one has to choose one of the following child classes:
   - pyramids (frusta):
     * rectangular
     * trigonal
-    * quadratic: [Pyramid4](hard/pyramid4), Bipyramid4
+    * quadratic: Pyramid4, Bipyramid4
     * hexagonal
   - other polyhedra:
 - soft particles:
@@ -60,7 +60,7 @@ particle = ba.Particle(material_Particle, ff)
 
 Form factor catalogues in earlier software:
 - IsGISAXS: [Lazzari 2006](/lit/lazzari2006) (manual),
-  [Renaud et al 2009](/lit/Renaud2009) (review).
+  [Renaud et al 2009](/lit/renaud2009) (review).
 - FitGISAXS: [Babonneau 2010](/lit/babonneau2010) (paper),
   [Babonneau 2013](/lit/babonneau2013) (software archive).
 
diff --git a/hugo/content/ref/sample/particle/ff/hard/bipyramid4.md b/hugo/content/ref/sample/particle/ff/hard/bipyramid4.md
index c541c6bd6b6e0759870206b9cb0a78934407dd4d..c76a756dc1ac2d9f49919bc7f66d765559cb3607 100644
--- a/hugo/content/ref/sample/particle/ff/hard/bipyramid4.md
+++ b/hugo/content/ref/sample/particle/ff/hard/bipyramid4.md
@@ -33,7 +33,7 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "Bipyramid4" %}} inherits from the interface class
+Class [Bipyramid4]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
 {{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor computation is based on the generic form factor of a polyhedron
diff --git a/hugo/content/ref/sample/particle/ff/hard/box.md b/hugo/content/ref/sample/particle/ff/hard/box.md
index 98a0d74b19b48de4c5b6f17d592795e5fd242179..ac5018229d035f1960a80ec7862f4c74312786ea 100644
--- a/hugo/content/ref/sample/particle/ff/hard/box.md
+++ b/hugo/content/ref/sample/particle/ff/hard/box.md
@@ -27,7 +27,7 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "Box" %}} inherits from the interface class
+Class [Box]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
 {{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor is computed as
diff --git a/hugo/content/ref/sample/particle/ff/hard/cantellatedcube.md b/hugo/content/ref/sample/particle/ff/hard/cantellatedcube.md
index 6fce74105b5ef746037a155a2191ed9bf86cc188..2d96a849d5c4498ffb00eea089f2b29edab6a594 100644
--- a/hugo/content/ref/sample/particle/ff/hard/cantellatedcube.md
+++ b/hugo/content/ref/sample/particle/ff/hard/cantellatedcube.md
@@ -32,7 +32,7 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "CantellatedCube" %}} inherits from the interface class
+Class [CantellatedCube]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
 {{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor computation is based on the generic form factor of a polyhedron with inversion symmetry provided by {{% link-libformfactor %}}.
diff --git a/hugo/content/ref/sample/particle/ff/hard/dodecahedron.md b/hugo/content/ref/sample/particle/ff/hard/dodecahedron.md
index e94459396aef95e0d4c402929e860c711b01aa4b..37c3ad1d13e8640f7c5928866e73774f2f8bca44 100644
--- a/hugo/content/ref/sample/particle/ff/hard/dodecahedron.md
+++ b/hugo/content/ref/sample/particle/ff/hard/dodecahedron.md
@@ -28,8 +28,8 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "Dodecahedron" %}} inherits from the interface class
-{{% ref-class "Sample/Particle" "IFormFactor" %}}.).
+Class [Dodecahedron]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
+{{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor computation is based on the generic form factor of a polyhedron with inversion symmetry provided by {{% link-libformfactor %}}.
 
diff --git a/hugo/content/ref/sample/particle/ff/hard/icosahedron.md b/hugo/content/ref/sample/particle/ff/hard/icosahedron.md
index 8b41794df9b10f1ec1c3009c01ef5d10fa13c2d2..67c64052c4ebf399873014b00307c976a198b8ad 100644
--- a/hugo/content/ref/sample/particle/ff/hard/icosahedron.md
+++ b/hugo/content/ref/sample/particle/ff/hard/icosahedron.md
@@ -28,7 +28,7 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "Icosahedron" %}} inherits from the interface class
+Class [Icosahedron]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
 {{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor computation is based on the generic form factor of a polyhedron with inversion symmetry provided by {{% link-libformfactor %}}.
diff --git a/hugo/content/ref/sample/particle/ff/hard/platonicoctahedron.md b/hugo/content/ref/sample/particle/ff/hard/platonicoctahedron.md
index 65f643415dbef564d1ed731e09703d41f4021f4f..0cd94bc5f33f622a140ab96f3ab1b438384de0fa 100644
--- a/hugo/content/ref/sample/particle/ff/hard/platonicoctahedron.md
+++ b/hugo/content/ref/sample/particle/ff/hard/platonicoctahedron.md
@@ -28,7 +28,7 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "PlatonicOctahedron" %}} inherits from the interface class
+Class [PlatonicOctahedron]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
 {{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor computation is based on the generic form factor of a polyhedron provided by {{% link-libformfactor %}}.
diff --git a/hugo/content/ref/sample/particle/ff/hard/platonictetrahedron.md b/hugo/content/ref/sample/particle/ff/hard/platonictetrahedron.md
index 7740a0cb3626e1b354e8d62af8bab2f3758df95a..d574a83ab1e1965d85ee6a5908ba481e1134e409 100644
--- a/hugo/content/ref/sample/particle/ff/hard/platonictetrahedron.md
+++ b/hugo/content/ref/sample/particle/ff/hard/platonictetrahedron.md
@@ -29,7 +29,7 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "PlatonicTetrahedron" %}} inherits from the interface class
+Class [PlatonicTetrahedron]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
 {{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor computation is based on the generic form factor of a polyhedron provided by {{% link-libformfactor %}}.
diff --git a/hugo/content/ref/sample/particle/ff/hard/prism3.md b/hugo/content/ref/sample/particle/ff/hard/prism3.md
index 2fb5a9a53f0b89744cddcd45fb13aef73fd6ceed..40497991af17586b53d06306d11153061544ae79 100644
--- a/hugo/content/ref/sample/particle/ff/hard/prism3.md
+++ b/hugo/content/ref/sample/particle/ff/hard/prism3.md
@@ -26,7 +26,7 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "Prism3" %}} inherits from the interface class
+Class [Prism3]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
 {{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor is computed as
diff --git a/hugo/content/ref/sample/particle/ff/hard/prism6.md b/hugo/content/ref/sample/particle/ff/hard/prism6.md
index 1f7aeb7af7271dd33de738c010fdd3c5c93d3f88..4b061c02f15fce049e878f7745ef1fec88cca30d 100644
--- a/hugo/content/ref/sample/particle/ff/hard/prism6.md
+++ b/hugo/content/ref/sample/particle/ff/hard/prism6.md
@@ -26,7 +26,7 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "Prism6" %}} inherits from the interface class
+Class [Prism6]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
 {{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor is computed as
diff --git a/hugo/content/ref/sample/particle/ff/hard/pyramid2.md b/hugo/content/ref/sample/particle/ff/hard/pyramid2.md
index 388ce26321504be73dd759035c8feae0d8cf6f12..bc0e0abfdb151a01e7ac50a5edfc1938d78d8ce2 100644
--- a/hugo/content/ref/sample/particle/ff/hard/pyramid2.md
+++ b/hugo/content/ref/sample/particle/ff/hard/pyramid2.md
@@ -32,7 +32,7 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "Pyramid2" %}} inherits from the interface class
+Class [Pyramid2]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
 {{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor computation is based on the generic form factor of a polyhedron
diff --git a/hugo/content/ref/sample/particle/ff/hard/pyramid3.md b/hugo/content/ref/sample/particle/ff/hard/pyramid3.md
index 7f08b838abda8a62bcdc0c5d460a8c4edd677c22..b007c4048e5c04c85a2da2b9eaa10690614412f6 100644
--- a/hugo/content/ref/sample/particle/ff/hard/pyramid3.md
+++ b/hugo/content/ref/sample/particle/ff/hard/pyramid3.md
@@ -34,7 +34,7 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "Pyramid3" %}} inherits from the interface class
+Class [Pyramid3]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
 {{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor computation is based on the generic form factor of a polyhedron
@@ -48,7 +48,7 @@ $$ V=\dfrac{L^3\tan\alpha}{24}\Big[1-\Big(1-\dfrac{2\sqrt3H}{L\tan\alpha}\Big)^3
 
 More special:
 - [Prism3](/ref/sample/particle/ff/hard/prism3), if $\alpha=90^{\circ}$.
-- [PlatonicTetrahedron](/ref/sample/particle/ff/hard/platonitetrahedron), if regular and not truncated.
+- [PlatonicTetrahedron](/ref/sample/particle/ff/hard/platonictetrahedron), if regular and not truncated.
 
 #### Example
 
diff --git a/hugo/content/ref/sample/particle/ff/hard/pyramid4.md b/hugo/content/ref/sample/particle/ff/hard/pyramid4.md
index b1162eed96acb3b43c2819f010f262b909dba5b6..6922913be0efad517750c1b33eb937baf1bf680b 100644
--- a/hugo/content/ref/sample/particle/ff/hard/pyramid4.md
+++ b/hugo/content/ref/sample/particle/ff/hard/pyramid4.md
@@ -31,7 +31,7 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "Pyramid4" %}} inherits from the interface class
+Class [Pyramid4]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
 {{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor computation is based on the generic form factor of a polyhedron
diff --git a/hugo/content/ref/sample/particle/ff/hard/pyramid6.md b/hugo/content/ref/sample/particle/ff/hard/pyramid6.md
index e973473430eda2b8ab05007d2ad2ad45c1c144a7..bbcb26fcbd983e4058594530994678a93e0e149b 100644
--- a/hugo/content/ref/sample/particle/ff/hard/pyramid6.md
+++ b/hugo/content/ref/sample/particle/ff/hard/pyramid6.md
@@ -33,7 +33,7 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "Pyramid6" %}} inherits from the interface class
+Class [Pyramid6]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
 {{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor computation is based on the generic form factor of a polyhedron
diff --git a/hugo/content/ref/sample/particle/ff/hard/sphere.md b/hugo/content/ref/sample/particle/ff/hard/sphere.md
index b8f1e00919691519d2e15129339bd10584005c59..0493a23083a55ba7780d926195563995fcfd674a 100644
--- a/hugo/content/ref/sample/particle/ff/hard/sphere.md
+++ b/hugo/content/ref/sample/particle/ff/hard/sphere.md
@@ -6,7 +6,7 @@ title = "Sphere"
 
 A full sphere.
 
-<img src="/img/draw/ff/3d/Sphere.png" width="30%" >
+<img src="/img/draw/ff/3d/FullSphere.png" width="30%" >
 <img src="/img/draw/ff/2d/Sphere_xy.svg" width="30%">
 <img src="/img/draw/ff/2d/Sphere_xz.svg" width="30%">
 
@@ -43,7 +43,7 @@ $$ V=\dfrac{4\pi}{3} R^3. $$
 #### Related shapes
 
 More general:
-- [Spheroid](/ref/sample/particle/ff/hard/fullspheroid), if ellipse in vertical cross section.
+- [Spheroid](/ref/sample/particle/ff/hard/spheroid), if ellipse in vertical cross section.
 - [TruncatedSphere](/ref/sample/particle/ff/hard/truncatedsphere), if truncated from the top and/or the bottom.
 
 #### Example
diff --git a/hugo/content/ref/sample/particle/ff/hard/spheroid.md b/hugo/content/ref/sample/particle/ff/hard/spheroid.md
index fdf09f9196c175c8dbd7707d16e185401ca13263..dfaab3483fbf7edc4669004d9651ee73712d2fe1 100644
--- a/hugo/content/ref/sample/particle/ff/hard/spheroid.md
+++ b/hugo/content/ref/sample/particle/ff/hard/spheroid.md
@@ -6,7 +6,7 @@ title = "Spheroid"
 
 A full spheroid, generated by rotating an ellipse around the vertical axis.
 
-<img src="../3d/Spheroid.png" width="30%" >
+<img src="/img/draw/ff/3d/Spheroid.png" width="30%" >
 <img src="/img/draw/ff/2d/Spheroid_xy.svg" width="30%">
 <img src="/img/draw/ff/2d/Spheroid_xz.svg" width="30%">
 
@@ -42,7 +42,7 @@ $$ V=\dfrac{2\pi}{3} R^2H. $$
 #### Related shapes
 
 More special:
-- [Sphere](/ref/sample/particle/ff/hard/fullsphere), if $H=2R.$
+- [Sphere](/ref/sample/particle/ff/hard/sphere), if $H=2R.$
 
 More general:
 - [TruncatedSpheroid](/ref/sample/particle/ff/hard/truncatedspheroid), if truncated from the top and/or the bottom.
@@ -61,4 +61,4 @@ Replicates the "Full spheroid" in IsGISAXS [[manual](/lit/lazzari2006), Eq. 2.36
 factors of 2 in their volume formula and form factor implementation, and "Spheroid" in FitGISAXS [[Babonneau 2013](/lit/babonneau2013)]. Up to BornAgain
 1.16, our form factor computation followed IsGISAXS in using numeric integration in
 the $z$ coordinate.
-In BornAgain, named "FullSpheroid" up to version 1.19.
\ No newline at end of file
+In BornAgain, named "FullSpheroid" up to version 1.19.
diff --git a/hugo/content/ref/sample/particle/ff/hard/truncatedcube.md b/hugo/content/ref/sample/particle/ff/hard/truncatedcube.md
index 089f686624e4a81bf01b0c2a5957602f7424fcca..81e833faa202201707cbf7bf2d8d4c2787a2cdb7 100644
--- a/hugo/content/ref/sample/particle/ff/hard/truncatedcube.md
+++ b/hugo/content/ref/sample/particle/ff/hard/truncatedcube.md
@@ -31,7 +31,7 @@ As for any other [Form factor](/ref/sample/particle/ff).
 
 #### Implementation
 
-Class {{% ref-class "Sample/HardParticle" "TruncatedCube" %}} inherits from the interface class
+Class [TruncatedCube]({{% url-src %}}/Sample/HardParticle/Polyhedra.h) inherits from the interface class
 {{% ref-class "Sample/Particle" "IFormFactor" %}}.
 
 Form factor computation is based on the generic form factor of a polyhedron
diff --git a/hugo/content/ref/sim/class/scattering/index.md b/hugo/content/ref/sim/class/scattering/index.md
index fbe8131f1507acac2d8f07d8841e8a6fb321c5bd..7684a00331a5b1560fa9cf0be6e98b23174dffe3 100644
--- a/hugo/content/ref/sim/class/scattering/index.md
+++ b/hugo/content/ref/sim/class/scattering/index.md
@@ -17,7 +17,7 @@ result = simulation.simulate()
 ```
 
 For the constructor arguments, see sections [beam](/ref/instr/beam),
-[sample](/ref/sample), and [detector](/py/instr/det).
+[sample](/ref/sample), and [detector](/ref/instr/det).
 
 For optional settings, see [simulation options](/ref/sim/setup/options).
 
diff --git a/hugo/content/ref/sim/class/specular/index.md b/hugo/content/ref/sim/class/specular/index.md
index 8daa1aa228355ab827d4b7ffd36a42df645bb95b..94a4cf27d85eb52dc70a9c793e4a1ae0c4009272 100644
--- a/hugo/content/ref/sim/class/specular/index.md
+++ b/hugo/content/ref/sim/class/specular/index.md
@@ -27,10 +27,12 @@ see [Datafield](/ref/sim/simulation-result).
 ##### Examples
 
 * [basic specular simulation](/ex/sim/specular)
+* [specular signal from a rough sample](/ex/sample/roughness/specular_default)
+* [real-life fitting: Pt layer](/ex/fit/reflectometry-pt-layer)
+* [real-life fitting: magnetic lattice](/ex/fit/reflectometry-honeycomb)
 
 ##### Further reading
 
-* [specular signal from a rough sample](/ref/sample/roughness/specular/index.md)
-* [beam footprint correction](/ref/instr/beam/footprint/index.md)
-* [beam divergence in specular simulations](/ref/instr/beam/full-divergence/index.md)
-* [fitting reflectometry data](/ex/fit/extended/fit-specular-data/index.md)
+* [beam footprint correction](/ref/instr/beam/footprint)
+* [beam divergence in specular simulations](/ref/instr/beam/divergence)
+* [basic roughness tutorial](/ref/sample/roughness)
diff --git a/hugo/content/ref/sim/setup/options/_index.md b/hugo/content/ref/sim/setup/options/_index.md
index 22c1ba1c19e49d7255365ab70c81da65f363e037..c510dd227577d45f5411a7900220e182d6d8e4aa 100644
--- a/hugo/content/ref/sim/setup/options/_index.md
+++ b/hugo/content/ref/sim/setup/options/_index.md
@@ -10,6 +10,6 @@ SimulationOptions object. This object can be modified
 through the following setter functions:
 
 - [setMonteCarloIntegration(_switch_, _n_)](mc)
-- [setNumberOfThreads(_n_)](nthreads)
+- [setNumberOfThreads(_n_)](threads)
 - [setIncludeSpecular(_switch_)](specular)
 - [setUseAvgMaterials(_switch_)](avgmat)
diff --git a/hugo/hugo.toml b/hugo/hugo.toml
index 3bc2a103dcb76c5d5812d3956788383c4b762def..bdd9be995c3b02ac9039d5452c24ea8e7a2c4313 100644
--- a/hugo/hugo.toml
+++ b/hugo/hugo.toml
@@ -28,6 +28,7 @@ PygmentsStyle = "vs"
 
   # for links to source repository
   url_blob = "https://jugit.fz-juelich.de/mlz/bornagain/-/blob/main"
+  data_dir = "testdata"
 
   # currently unused
   url_doxy = "https://bornagainproject.org/ext/api/git-main/user-API"
diff --git a/hugo/layouts/shortcodes/ref-data.html b/hugo/layouts/shortcodes/ref-data.html
new file mode 100644
index 0000000000000000000000000000000000000000..eff640aadf6ce05437f2eececfee779fb07e842b
--- /dev/null
+++ b/hugo/layouts/shortcodes/ref-data.html
@@ -0,0 +1 @@
+[{{ .Get 0}}]({{.Site.Params.url_blob}}/{{.Site.Params.data_dir}}/{{ .Get 0}})
diff --git a/hugo/static/img/draw/ff/3d/Sphere.png b/hugo/static/img/draw/ff/3d/Sphere.png
deleted file mode 100644
index f904e65cbec0e44d40c407e420f663365d44b203..0000000000000000000000000000000000000000
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diff --git a/hugo/static/img/draw/ff/3d/FullSpheroid.png b/hugo/static/img/draw/ff/3d/Spheroid.png
similarity index 100%
rename from hugo/static/img/draw/ff/3d/FullSpheroid.png
rename to hugo/static/img/draw/ff/3d/Spheroid.png