From bf015da8a1b404ce9d4161c6ce1d56b187a82377 Mon Sep 17 00:00:00 2001
From: Sergi Siso <sergiesg@gmail.com>
Date: Wed, 16 Jul 2025 14:44:03 +0100
Subject: [PATCH 01/11] #3058 Update linkcheck parameters

---
 .github/workflows/linkcheck.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml
index 296e259e04..1dc2224069 100644
--- a/.github/workflows/linkcheck.yml
+++ b/.github/workflows/linkcheck.yml
@@ -12,5 +12,6 @@ jobs:
         with:
           github_token: ${{ secrets.github_token }}
           reporter: github-pr-check
-          fail_on_error: true
           config_file: '.github/linkspector.yml'
+          fail_level: any
+          show_stats: true

From 88070e419eea3a224b3909c028e82e5feaad78f8 Mon Sep 17 00:00:00 2001
From: Sergi Siso <sergiesg@gmail.com>
Date: Wed, 16 Jul 2025 14:50:07 +0100
Subject: [PATCH 02/11] #3058 Change linkcheck parameter

---
 .github/workflows/linkcheck.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml
index 1dc2224069..84e9f7381b 100644
--- a/.github/workflows/linkcheck.yml
+++ b/.github/workflows/linkcheck.yml
@@ -13,5 +13,5 @@ jobs:
           github_token: ${{ secrets.github_token }}
           reporter: github-pr-check
           config_file: '.github/linkspector.yml'
-          fail_level: any
+          fail_level: error
           show_stats: true

From 5bb39faca5a9a70813eb8c53bdc2e7866ae1fefd Mon Sep 17 00:00:00 2001
From: Sergi Siso <sergiesg@gmail.com>
Date: Wed, 16 Jul 2025 14:55:34 +0100
Subject: [PATCH 03/11] #3058 Change linkcheck parameters

---
 .github/workflows/linkcheck.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml
index 84e9f7381b..fba7396195 100644
--- a/.github/workflows/linkcheck.yml
+++ b/.github/workflows/linkcheck.yml
@@ -13,5 +13,6 @@ jobs:
           github_token: ${{ secrets.github_token }}
           reporter: github-pr-check
           config_file: '.github/linkspector.yml'
-          fail_level: error
+          fail_on_error: true
+          filter-mode: nofilter
           show_stats: true

From f2fb1f5c2864300aaa7eb2b39a55cf17c593c8b0 Mon Sep 17 00:00:00 2001
From: Sergi Siso <sergiesg@gmail.com>
Date: Wed, 16 Jul 2025 14:59:36 +0100
Subject: [PATCH 04/11] Change linkcheck parameters

---
 .github/workflows/linkcheck.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml
index fba7396195..f8f293573c 100644
--- a/.github/workflows/linkcheck.yml
+++ b/.github/workflows/linkcheck.yml
@@ -12,7 +12,7 @@ jobs:
         with:
           github_token: ${{ secrets.github_token }}
           reporter: github-pr-check
-          config_file: '.github/linkspector.yml'
           fail_on_error: true
-          filter-mode: nofilter
+          config_file: '.github/linkspector.yml'
+          filter_mode: nofilter
           show_stats: true

From dadcd532fb3ca6d91b134d5dec6265fa2765bb22 Mon Sep 17 00:00:00 2001
From: Sergi Siso <sergiesg@gmail.com>
Date: Wed, 16 Jul 2025 16:02:51 +0100
Subject: [PATCH 05/11] Fix some links from READMEs

---
 .github/linkspector.yml                           |  2 ++
 README.md                                         | 13 +++++++------
 tutorial/practicals/generic/2_profiling/README.md |  6 +++---
 tutorial/practicals/generic/3_openmp/README.md    |  2 +-
 tutorial/practicals/generic/4_openacc/README.md   | 11 ++++-------
 5 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/.github/linkspector.yml b/.github/linkspector.yml
index 8d84d6dfb3..2b1c158d38 100644
--- a/.github/linkspector.yml
+++ b/.github/linkspector.yml
@@ -3,6 +3,8 @@ dirs:
 useGitIgnore: true
 ignorePatterns:
   - pattern: '^https://mybinder.org/v2/gh/stfc/psyclone'
+  - pattern: '^https://codecov.io/gh/stfc/PSyclone'
+  - pattern: '^\.'
 replacementPatterns:
   - pattern: '^https:\/\/(psyclone.*\.readthedocs\.io\/en)\/stable$'
     replacement: 'https://$1/latest'
diff --git a/README.md b/README.md
index 560a82b6dd..11323f9e92 100644
--- a/README.md
+++ b/README.md
@@ -20,18 +20,18 @@ DSLs following the PSyKAl model developed in the
 [GungHo project](https://www.metoffice.gov.uk/research/foundation/dynamics/next-generation).
 
 PSyclone is currently used to support the [LFRic mixed finite-element PSyKAl
-DSL](https://psyclone.readthedocs.io/en/latest/lfric.html)
+DSL](https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html)
 for the [UK MetOffice's next generation modelling
 system](https://www.metoffice.gov.uk/research/modelling-systems/lfric/) and
 the [GOcean finite-difference PSyKAl
-DSL](https://psyclone.readthedocs.io/en/latest/gocean1p0.html) for a [prototype
+DSL](https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html) for a [prototype
 2D ocean modelling system](https://gtr.ukri.org/projects?ref=NE%2FL01209X%2F1).
 It is also used to [insert GPU offloading
-directives](https://psyclone.readthedocs.io/en/latest/nemo.html) into existing
+directives](https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/nemo_examples.html) into existing
 directly-addressed MPI applications such as the
 [NEMO ocean model](https://www.nemo-ocean.eu/).
 
-For more detailed information see the [PSyclone Documentation](http://psyclone.readthedocs.io).
+For more detailed information see the [PSyclone Documentation](http://psyclone.readthedocs.io/en/latest).
 
 # Installation #
 
@@ -60,8 +60,9 @@ PSyclone is also available in the
 [Spack](https://packages.spack.io/package.html?name=py-psyclone) package
 managers.
 
-For more information about the installation process see
-[this section of the User Guide](https://psyclone.readthedocs.io/en/latest/system_specific_setup.html).
+For more information about the installation process see the
+[Getting Going](https://psyclone.readthedocs.io/en/latest/user_guide/getting_going.html).
+section of the User Guide.
 
 <!---  TODO #2627
 # Try it on Binder #
diff --git a/tutorial/practicals/generic/2_profiling/README.md b/tutorial/practicals/generic/2_profiling/README.md
index acac5156ef..79faed5311 100644
--- a/tutorial/practicals/generic/2_profiling/README.md
+++ b/tutorial/practicals/generic/2_profiling/README.md
@@ -8,8 +8,8 @@ driver program. The reason for this will become clear as you work
 through the tutorial.
 
 You can find information on the various transformations supported by
-PSyclone in the [User Guide](https://psyclone.readthedocs.io/en/latest/transformations.html).
-There is a separate [section](https://psyclone.readthedocs.io/en/latest/profiling.html) on
+PSyclone in the [User Guide](https://psyclone.readthedocs.io/en/latest/user_guide/transformations.html).
+There is a separate [section](https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html) on
 PSyclone's support for profiling.
 
 ## Prerequisites ##
@@ -22,7 +22,7 @@ Make then you may need to edit the Makefile and replace the occurrences of
 ## 1. Automatic Profiling ##
 
 To begin, we will make use of PSyclone's support for the
-[automatic addition of profiling instrumentation](https://psyclone.readthedocs.io/en/latest/profiling.html). For
+[automatic addition of profiling instrumentation](https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html). For
 demonstration purposes we will be using the 'simple-timing' library
 distributed with PSyclone since that has no dependencies. (PSyclone
 currently provides wrapper libraries for profiling tools such as
diff --git a/tutorial/practicals/generic/3_openmp/README.md b/tutorial/practicals/generic/3_openmp/README.md
index 8fe7d807b5..e66c79654a 100644
--- a/tutorial/practicals/generic/3_openmp/README.md
+++ b/tutorial/practicals/generic/3_openmp/README.md
@@ -7,7 +7,7 @@ uses PSyclone to parallelise the tracer-advection mini-app to make
 use of a multi-core CPU by adding appropriate OpenMP directives.
 
 You can find information on the various transformations supported by
-PSyclone in the [User Guide](https://psyclone.readthedocs.io/en/latest/transformations.html).
+PSyclone in the [User Guide](https://psyclone.readthedocs.io/en/latest/user_guide/transformations.html#openmp).
 
 ## Prerequisites ##
 
diff --git a/tutorial/practicals/generic/4_openacc/README.md b/tutorial/practicals/generic/4_openacc/README.md
index d9204019ba..d8d950ae61 100644
--- a/tutorial/practicals/generic/4_openacc/README.md
+++ b/tutorial/practicals/generic/4_openacc/README.md
@@ -7,10 +7,8 @@ mini-app. When built with a suitable compiler this then enables the
 code to be run on a GPU (but this is not required for this tutorial).
 
 You may find it helpful to read the section on
-[OpenACC](https://psyclone.readthedocs.io/en/latest/transformations.html?highlight=accdatatrans#openacc)
-in the
-[Transformations](https://psyclone.readthedocs.io/en/latest/transformations.html?highlight=accdatatrans#transformations)
-section of the PSyclone User Guide.
+[OpenACC](https://psyclone.readthedocs.io/en/latest/user_guide/transformations.html#openacc)
+Transformations page of the PSyclone User Guide.
 
 The OpenACC specification may be found at https://www.openacc.org/specification.
 
@@ -388,9 +386,8 @@ add the necessary option to add the `COLLAPSE` clause.
    ```
 
 4. How do we add the `COLLAPSE` clause? If we look at the documentation
-   for `ACCLoopTrans` in the
-   [Transformations](https://psyclone.readthedocs.io/en/latest/transformations.html?highlight=accdatatrans#transformations)
-   section of the User Guide, we see that it takes an `options`
+   for [ACCLoopTrans](https://psyclone.readthedocs.io/en/latest/_autogenerated/autoapi/psyclone.transformations.html#psyclone.transformations.ACCLoopTrans)
+   , we see that it takes an `options`
    dictionary argument. We can therefore specify that we want
    `COLLAPSE(2)` by doing:
    ```python

From db49b0cc1535a08f62db2ad61493f9138c3d887e Mon Sep 17 00:00:00 2001
From: Sergi Siso <sergiesg@gmail.com>
Date: Wed, 16 Jul 2025 16:34:57 +0100
Subject: [PATCH 06/11] Fix more links

---
 lib/README.md                                 |  8 +++---
 .../LFRic_kernel_structure.md                 | 14 +++++------
 .../building_code/1_simple_kernels/README.md  |  2 +-
 .../1_simple_kernels/part1/README.md          |  2 +-
 .../1_simple_kernels/part2/README.md          |  4 +--
 .../LFRic/building_code/2_built_ins/README.md | 25 +++++++++----------
 .../building_code/3_time_evolution/README.md  |  6 ++---
 .../practicals/LFRic/building_code/README.md  | 15 ++++++-----
 .../building_code/background/LFRic_intro.md   |  2 +-
 .../background/LFRic_structure.md             | 16 ++++++------
 .../3_overlapping_comms/README.md             |  4 +--
 .../distributed_memory/4_reductions/README.md |  2 +-
 .../generic/1_intro_psyir/README.md           |  2 +-
 13 files changed, 50 insertions(+), 52 deletions(-)

diff --git a/lib/README.md b/lib/README.md
index 2ed73e6e5c..2b6108bb78 100644
--- a/lib/README.md
+++ b/lib/README.md
@@ -80,7 +80,7 @@ Fortran compiler (``gfortran``), i.e. simply running ``make`` will build a
 wrapper library with the version of ``gfortran`` available in a user's
 environment. The compilation flags vary from one library to another (they
 are usually set to debugging). As for the compilation of the [API examples](
-https://psyclone.readthedocs.io/en/latest/examples.html#compilation), these
+https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/examples_intro.html#compilation), these
 flags can be set to a different compiler. For instance,
 
 ```shell
@@ -88,7 +88,7 @@ F90=ifort F90FLAGS="-g -check bounds" make
 ```
 
 Similar to compilation of the [examples](
-https://psyclone.readthedocs.io/en/latest/examples.html#compilation), the
+https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/examples_intro.html#compilation), the
 compiled library can be removed by running ``make clean``. There is also
 the ``allclean`` target that removes the compiled wrapper library as well
 as the compiled infrastructure library that the wrapper may
@@ -96,7 +96,7 @@ as the compiled infrastructure library that the wrapper may
 
 The compilation of wrapper libraries was tested with the Gnu and Intel
 Fortran compilers, see [here](
-https://psyclone.readthedocs.io/en/latest/examples.html#supported-compilers)
+https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/examples_intro.html#supported-compilers)
 for the full list. Please let the PSyclone developers know if you have
 problems using a compiler that has been tested or if you are working
 with a different compiler.
@@ -118,7 +118,7 @@ to the API they are used for. [GOcean API](
 https://psyclone.readthedocs.io/en/stable/gocean1p0.html) uses the
 [``dl_esm_inf`` library](https://github.com/stfc/dl_esm_inf) and
 [LFRic API](
-https://psyclone.readthedocs.io/en/latest/lfric.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html)
 uses the LFRic infrastructure (see the linked documentation on how to
 access and use the LFRic code). The locations of the respective
 infrastructure libraries can be configured with the variables
diff --git a/tutorial/practicals/LFRic/building_code/1_simple_kernels/LFRic_kernel_structure.md b/tutorial/practicals/LFRic/building_code/1_simple_kernels/LFRic_kernel_structure.md
index 7af41fefc0..560a237145 100644
--- a/tutorial/practicals/LFRic/building_code/1_simple_kernels/LFRic_kernel_structure.md
+++ b/tutorial/practicals/LFRic/building_code/1_simple_kernels/LFRic_kernel_structure.md
@@ -94,9 +94,9 @@ of an individual kernel type. They come in two main forms: derived types
 such as `operates_on` above or arrays). Here we briefly explain the contents
 of the `arg_type` and `operates_on` metadata. For more information please refer
 to the [*Metadata* section](
-https://psyclone.readthedocs.io/en/latest/lfric.html#metadata)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#metadata)
 of the LFRic API [user documentation](
-https://psyclone.readthedocs.io/en/latest/lfric.html).
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html).
 
 The `arg_type` in this example describes the two (hence `dimension(2)`)
 arguments that this kernel operates on:
@@ -109,9 +109,9 @@ arguments that this kernel operates on:
 The `GH_` prefix comes from "GungHo", the name of the dynamical core used in
 the LFRic model. Please refer to the documentation for more information on
 [supported accesses](
-https://psyclone.readthedocs.io/en/latest/lfric.html#valid-access-modes)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#valid-access-modes)
 and [function spaces](
-https://psyclone.readthedocs.io/en/latest/lfric.html#supported-function-spaces)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#supported-function-spaces)
 for the LFRic data objects.
 
 The `operates_on` metadata specifies how LFRic kernels are called
@@ -204,15 +204,15 @@ The order of kernel arguments roughly corresponds to the order of
 ordering arguments is to put arguments that are written to first.
 The full PSyclone LFRic API specification of the argument ordering for
 the [general LFRic user-defined kernels](
-https://psyclone.readthedocs.io/en/latest/lfric.html#rules-for-general-purpose-kernels)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#rules-for-general-purpose-kernels)
 is quite complex, hence making the [PSyclone kernel tool](
-https://psyclone.readthedocs.io/en/stable/psyclone_kern.html) very useful
+https://psyclone.readthedocs.io/en/latest/user_guide/psyclone_kern.html) very useful
 for development.
 
 LFRic kernels can update more than one field and/or operator arguments.
 However, scalar arguments in user-defined LFRic kernels must be
 [read-only](
-https://psyclone.readthedocs.io/en/latest/lfric.html#valid-access-modes).
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#valid-access-modes).
 
 ---
 
diff --git a/tutorial/practicals/LFRic/building_code/1_simple_kernels/README.md b/tutorial/practicals/LFRic/building_code/1_simple_kernels/README.md
index 67655add1f..4105bbbe79 100644
--- a/tutorial/practicals/LFRic/building_code/1_simple_kernels/README.md
+++ b/tutorial/practicals/LFRic/building_code/1_simple_kernels/README.md
@@ -16,7 +16,7 @@ There are two parts of this tutorial and each should be done in turn.
 
 *Note:* For more information on the supported LFRic function spaces in
 PSyclone please refer to this PSyclone [user guide section](
-https://psyclone.readthedocs.io/en/latest/lfric.html#supported-function-spaces).
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#lfric-function-space).
 
 Each kernel in this tutorial performs one simple mathematical operation
 in order to learn how to work with the basic building blocks of an
diff --git a/tutorial/practicals/LFRic/building_code/1_simple_kernels/part1/README.md b/tutorial/practicals/LFRic/building_code/1_simple_kernels/part1/README.md
index abc8d0e276..487fd8985a 100644
--- a/tutorial/practicals/LFRic/building_code/1_simple_kernels/part1/README.md
+++ b/tutorial/practicals/LFRic/building_code/1_simple_kernels/part1/README.md
@@ -95,7 +95,7 @@ becomes `setval_field_w3_`).
 The new kernel updates a field on a discontinuous function space
 `W3` so you will need to correct the access metadata for the updated
 field from `GH_INC` to `GH_READWRITE` (see [here](
-https://psyclone.readthedocs.io/en/latest/lfric.html#valid-access-modes)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#valid-access-modes)
 for more information of valid access modes depending on the function
 space that a field argument is defined on).
 
diff --git a/tutorial/practicals/LFRic/building_code/1_simple_kernels/part2/README.md b/tutorial/practicals/LFRic/building_code/1_simple_kernels/part2/README.md
index d76706e9af..568a73c1e3 100644
--- a/tutorial/practicals/LFRic/building_code/1_simple_kernels/part2/README.md
+++ b/tutorial/practicals/LFRic/building_code/1_simple_kernels/part2/README.md
@@ -47,13 +47,13 @@ field is to be updated (`GH_INC`) while the scalar is read only (`GH_READ`).
 the same as the access for an updated field on a continuous function
 space `W0` in [`setval_field_w0_kernel_mod.f90`](
 ../part1/setval_field_w0_kernel_mod.f90) (see [here](
-https://psyclone.readthedocs.io/en/latest/lfric.html#valid-access-modes)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#valid-access-modes)
 for more information of valid access modes depending on the function
 space that an argument is defined on). The generic function spaces are
 treated as continuous (the "worst case scenario") except in the case of
 a generic discontinuous function space `ANY_DISCONTINUOUS_SPACE_n`
 (see [here](
-https://psyclone.readthedocs.io/en/latest/lfric.html#supported-function-spaces)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#supported-function-spaces)
 for information on the supported function spaces).
 
 * Unlike the specific function space identifier `W0` that is located
diff --git a/tutorial/practicals/LFRic/building_code/2_built_ins/README.md b/tutorial/practicals/LFRic/building_code/2_built_ins/README.md
index 4e86367174..30e0a4db46 100644
--- a/tutorial/practicals/LFRic/building_code/2_built_ins/README.md
+++ b/tutorial/practicals/LFRic/building_code/2_built_ins/README.md
@@ -4,12 +4,12 @@ In the [first tutorial](../1_simple_kernels) we used [kernels](
 ../1_simple_kernels/LFRic_kernel_structure.md) for simple mathematical
 linear algebra operations, such as setting field to a value and adding fields.
 PSyclone provides [built-ins support](
-https://psyclone.readthedocs.io/en/stable/introduction_to_psykal.html#built-ins)
+https://psyclone.readthedocs.io/en/latest/user_guide/introduction_to_psykal.html#built-ins)
 for such simple operations.
 
 In this tutorial we will learn how to utilise the
 [LFRic API built-ins](
-https://psyclone.readthedocs.io/en/latest/lfric.html#built-ins)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#built-ins)
 support in PSyclone instead of using kernels. A quick introduction to
 built-ins is also given in the [section below](#quick-intro-to-built-ins).
 
@@ -119,26 +119,26 @@ This step consists of applying the following mathematical operations:
 The following built-ins need to be used for the operations above:
 
 * [`setval_c` built-in](
-  https://psyclone.readthedocs.io/en/latest/lfric.html#setval-c) for
+  https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#setval-c) for
   initialising (setting) fields to a scalar value (e.g. `field_out_w0 = 0`);
 
 * [`X_plus_Y` built-in](
-  https://psyclone.readthedocs.io/en/latest/lfric.html#x-plus-y)
+  https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#x-plus-y)
   for adding two fields (`field_out_w0 = field1_in_w0 + field2_in_w0`);
 
 * [`a_times_X` built-in](
-  https://psyclone.readthedocs.io/en/latest/lfric.html#a-times-x) for
+  https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#a-times-x) for
   multiplying a field by a scalar value (`field2_in_w3 = 2*field1_in_w3`);
 
 * [`X_minus_bY` built-in](
-  https://psyclone.readthedocs.io/en/latest/lfric.html#x-minus-by) for
+  https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#x-minus-by) for
   subtracting scaled fields (`field_out_w3 = field1_in_w3 - 0.5*field2_in_w3`).
 
 For more information on how the built-ins are named, look into the
 [*Naming scheme* section](
-https://psyclone.readthedocs.io/en/latest/lfric.html#naming-scheme)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#naming-scheme)
 of the [PSyclone LFRic API built-ins documentation](
-https://psyclone.readthedocs.io/en/latest/lfric.html#built-ins).
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#built-ins).
 
 The calls to some of the listed built-ins are outlined below:
 
@@ -330,8 +330,7 @@ run the executable
 ```
 
 The program prints out several log messages about setting up the model
-and calling the algorithm subroutine `builtins_alg`. As outlined
-[above](#algorithm-structure), the algorithm checks the minimum
+and calling the algorithm subroutine `builtins_alg`. The algorithm checks the minimum
 and maximum values of all fields after calling the built-ins to update
 them. The correct values for the output fields depend on the values you
 set the fields to (for instance, `field_w0_out` should return the
@@ -346,10 +345,10 @@ Similar to the user-defined [LFRic kernels](
 ../1_simple_kernels/LFRic_kernel_structure.md),
 the built-in kernels also have metadata but their metadata are defined in
 the PSyclone [LFRic API](
-https://psyclone.readthedocs.io/en/latest/lfric.html).
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html).
 
 Below is an example of metadata for the [built-in `X_plus_Y`](
-https://psyclone.readthedocs.io/en/latest/lfric.html#x-plus-y)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#x-plus-y)
 that adds two fields and stores the result in a third:
 
 ```fortran
@@ -376,5 +375,5 @@ fields passed to a built-in call **must be on the same function space**.
 Built-ins need to work with fields on any function space, hence using the
 `ANY_SPACE_1` identifier for the generic function space (see the
 [*Supported Function Spaces* section](
-https://psyclone.readthedocs.io/en/latest/lfric.html#lfric-function-space)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#lfric-function-space)
 for more information).
diff --git a/tutorial/practicals/LFRic/building_code/3_time_evolution/README.md b/tutorial/practicals/LFRic/building_code/3_time_evolution/README.md
index 4578b13a65..2077c46961 100644
--- a/tutorial/practicals/LFRic/building_code/3_time_evolution/README.md
+++ b/tutorial/practicals/LFRic/building_code/3_time_evolution/README.md
@@ -4,7 +4,7 @@ In the [first tutorial](../1_simple_kernels) we learned how to create and
 use [kernels](../1_simple_kernels/LFRic_kernel_structure.md) for
 mathematical operations on field data. In the [second tutorial](
 ../2_built_ins) we learned how to use [PSyclone built-ins](
-https://psyclone.readthedocs.io/en/latest/lfric.html#built-ins)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#built-ins)
 for simple linear algebra operations that update fields.
 
 In this tutorial we will build on this knowledge by using kernels for
@@ -133,7 +133,7 @@ below for more detailed information). The two exceptions are outlined below.
 
 The coordinate fields `chi(3)` in this tutorial are an example of a
 [field vector object](
-https://psyclone.readthedocs.io/en/latest/lfric.html#field-vector)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#field-vector)
 which is essentially a bundle of fields. The metadata representation
 of a field vector will be shown in the [*Step 1*](
 #step-1-complete-the-init_perturbation_kernel_modf90-kernel) below where
@@ -199,7 +199,7 @@ The first `arg_type` metadata descriptor is for the `perturbation` field on
 the `W3` function space that is updated (`GH_READWRITE` access for the
 discontinuous function spaces). The second `arg_type` descriptor is for the
 `chi(3)` coordinate [field vector](
-https://psyclone.readthedocs.io/en/latest/lfric.html#field-vector)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#field-vector)
 (see the [note above](#driver-structure)) on the same space as the
 `perturbation` field.
 
diff --git a/tutorial/practicals/LFRic/building_code/README.md b/tutorial/practicals/LFRic/building_code/README.md
index 60be5cdd95..a44158b79c 100644
--- a/tutorial/practicals/LFRic/building_code/README.md
+++ b/tutorial/practicals/LFRic/building_code/README.md
@@ -17,7 +17,7 @@ linked as needed in each tutorial.
 This tutorial shows how to create and use simple LFRic kernels to
 perform mathematical operations on the LFRic field data. It starts with
 different kernels for different LFRic finite-element [function spaces](
-https://psyclone.readthedocs.io/en/latest/lfric.html#supported-function-spaces)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#lfric-function-space)
 and uses them as a template to write generic kernels that can
 operate on any function space.
 
@@ -29,7 +29,7 @@ subroutine argument list and loops that update an LFRic field.
 ### [Tutorial 2: Built-ins](2_built_ins)
 
 This tutorial shows how to use the [PSyclone LFRic API built-ins](
-https://psyclone.readthedocs.io/en/latest/lfric.html#built-ins)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#built-ins)
 instead of kernels for simple linear algebra operations on fields.
 
 ### [Tutorial 3: Time evolution](3_time_evolution)
@@ -46,12 +46,11 @@ algorithms that need to be completed to propagate the field.
 This tutorial uses the previous [Time Evolution](#tutorial-3-time-evolution)
 example to show the usage of various
 PSyData transformations. [Kernel Extraction](
-https://psyclone.readthedocs.io/en/latest/psyke.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html)
 is the first transformation
-introduced, followed by [NAN verification](
-https://psyclone.readthedocs.io/en/latest/psy_data.html#psydata-nan-test)
+introduced, followed by NAN verification
 and [read-only-variable verification](
-https://psyclone.readthedocs.io/en/latest/psy_data.html#read-only-verification).
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html#value-range-check).
 All these examples are executable, and incorrect code can be uncommented to
 trigger the error checks enabled by some PSyData transformations.
 
@@ -64,7 +63,7 @@ that calls one or more [algorithms](
 background/LFRic_structure.md#algorithm-layer). The
 algorithms, in turn, contain `invoke` calls to one or more [kernels](
 background/LFRic_structure.md#kernel-layer) and/or [PSyclone built-ins](
-https://psyclone.readthedocs.io/en/latest/lfric.html#built-ins).
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#built-ins).
 
 The driver in each tutorial provides the framework to build an executable
 program through the set-up of the LFRic infrastructure objects and calls
@@ -102,7 +101,7 @@ It is advisable to run `make transform` whilst completing the kernel and
 and algorithm code to ensure that the code is correct. PSyclone checks
 that the source is syntactically correct and that it abides by the
 PSyclone [LFRIC API](
-https://psyclone.readthedocs.io/en/latest/lfric.html) rules.
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html) rules.
 
 ---
 
diff --git a/tutorial/practicals/LFRic/building_code/background/LFRic_intro.md b/tutorial/practicals/LFRic/building_code/background/LFRic_intro.md
index d3a3829405..b8b5367ba2 100644
--- a/tutorial/practicals/LFRic/building_code/background/LFRic_intro.md
+++ b/tutorial/practicals/LFRic/building_code/background/LFRic_intro.md
@@ -37,7 +37,7 @@ the Met Office and external LFRic developers and users.
 ### PSyclone in LFRic
 
 PSyclone LFRic API documentation can be found [here](
-https://psyclone.readthedocs.io/en/latest/lfric.html).
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html).
 
 LFRic wiki hosts pages on the use of PSyclone in LFRic, starting with the
 [PSyclone in LFRic wiki (requires login)](
diff --git a/tutorial/practicals/LFRic/building_code/background/LFRic_structure.md b/tutorial/practicals/LFRic/building_code/background/LFRic_structure.md
index 381e6bd1fa..643a6bb25e 100644
--- a/tutorial/practicals/LFRic/building_code/background/LFRic_structure.md
+++ b/tutorial/practicals/LFRic/building_code/background/LFRic_structure.md
@@ -26,7 +26,7 @@ done in the driver layer.
 
 *Note: See also the description of the LFRic Algorithm layer in the*
 [*PSyclone User Guide.*](
-https://psyclone.readthedocs.io/en/latest/lfric.html#algorithm)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#algorithm)
 
 LFRic algorithms perform mathematical operations on LFRic objects:
 **field**s, **operator**s and **scalar**s. Each of these objects
@@ -36,7 +36,7 @@ they will be referred to as "LFRic data objects".
 
 The important thing to note here is that algorithms (as well as other
 high-level code such as drivers) operate on [full objects](
-https://psyclone.readthedocs.io/en/stable/introduction_to_psykal.html#algorithm-layer) but
+https://psyclone.readthedocs.io/en/latest/user_guide/introduction_to_psykal.html#algorithm-layer) but
 **do not operate directly on object data** (or, in OO terminology, *must
 not break encapsulation*). The data is accessed in the [PSy layer](
 #psy-layer) via the required object accessor class, referred to as
@@ -57,12 +57,12 @@ can be `private` (if used only by the object) or `public`ly available
 
 LFRic algorithms manipulate data objects via `invoke` calls to
 [user-defined LFRic kernels](#kernel-layer) and [PSyclone built-ins](
-https://psyclone.readthedocs.io/en/latest/lfric.html#built-ins).
+https://psyclone.readthedocs.io/en/latest/user_guide/introduction_to_psykal.html#built-ins).
 The `invoke` calls are not standard Fortran calls. They are a way of
 specifying a sequence of kernels to call (with their associated
 arguments), prescribed by the DSL defined in the
 [PSyclone LFRic API](
-https://psyclone.readthedocs.io/en/latest/lfric.html). The use of
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html). The use of
 `invoke`s in LFRic is exclusive to the algorithm layer.
 
 Roughly speaking, the main parts of an LFRic algorithm are:
@@ -83,7 +83,7 @@ requirements in a time-stepping scheme).
 
 *Note: See also the description of the LFRic PSy layer in the*
 [*PSyclone User Guide.*](
-https://psyclone.readthedocs.io/en/latest/lfric.html#psy-layer)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#psy-layer)
 
 As explained in the [*Algorithm layer* section](#algorithm-layer),
 LFRic algorithms perform mathematical operations on LFRic data objects
@@ -93,7 +93,7 @@ LFRic kernels perform mathematical operations on a subset of data
 points of these objects.
 
 In the *Parallel Systems* or, in short, [PSy layer](
-https://psyclone.readthedocs.io/en/stable/introduction_to_psykal.html#psy-layer), PSyclone
+https://psyclone.readthedocs.io/en/latest/user_guide/introduction_to_psykal.html#psy-layer), PSyclone
 generates calls to the accessor classes for the LFRic data objects
 passed from the algorithm layer, referred to as `<class_name>_proxy`
 (e.g. `field_proxy`) and accesses the object data by dereferencing
@@ -109,10 +109,10 @@ The generated PSy-layer code in these tutorials is purely serial.
 
 *Note: See also the description of the LFRic Kernel layer in the*
 [*PSyclone User Guide.*](
-https://psyclone.readthedocs.io/en/latest/lfric.html#kernel)
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#kernel)
 
 LFRic kernels perform mathematical operations on [a subset of data points](
-https://psyclone.readthedocs.io/en/stable/introduction_to_psykal.html#kernel-layer)
+https://psyclone.readthedocs.io/en/latest/user_guide/introduction_to_psykal.html#kernel-layer)
 of LFRic data objects (fields, operators and scalars) passed
 from the [algorithm](#algorithm-layer) through the [PSy layer](#psy-layer).
 
diff --git a/tutorial/practicals/LFRic/distributed_memory/3_overlapping_comms/README.md b/tutorial/practicals/LFRic/distributed_memory/3_overlapping_comms/README.md
index 520d26c72c..6cb4e251bb 100644
--- a/tutorial/practicals/LFRic/distributed_memory/3_overlapping_comms/README.md
+++ b/tutorial/practicals/LFRic/distributed_memory/3_overlapping_comms/README.md
@@ -67,11 +67,11 @@ As transformations are objects we also need to create an instance of
 
 If you would like to find out more about this transformation, it is
 documented in the
-[User Guide](https://psyclone.readthedocs.io/en/latest/lfric.html)
+[User Guide](https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html)
 (search for `LFRicAsyncHaloExchangeTrans`).
 
 Traversing the PSyIR tree is discussed in the [user
-guide](https://psyclone.readthedocs.io/en/latest/psyir.html) (search
+guide](https://psyclone.readthedocs.io/en/latest/user_guide/psyir.html) (search
 for Tree Navigation) and in one of the [notebook
 tutorials](../../../../notebooks/introduction.ipynb).
 
diff --git a/tutorial/practicals/LFRic/distributed_memory/4_reductions/README.md b/tutorial/practicals/LFRic/distributed_memory/4_reductions/README.md
index 76e0ccb54a..b90c67aa38 100644
--- a/tutorial/practicals/LFRic/distributed_memory/4_reductions/README.md
+++ b/tutorial/practicals/LFRic/distributed_memory/4_reductions/README.md
@@ -14,7 +14,7 @@ reduction to the algorithm layer.
 As you have already learnt in a previous section of the tutorial,
 PSyclone provides a number of builtin kernels. Some of these kernels
 perform reductions. The builtins are specified in the PSyclone User Guide
-[here](https://psyclone.readthedocs.io/en/latest/lfric.html#built-ins).
+[here](https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html#built-ins).
 
 Choose one of the builtins that performs a reduction. These are either
 of the two inner products or the sum of elements builtins.
diff --git a/tutorial/practicals/generic/1_intro_psyir/README.md b/tutorial/practicals/generic/1_intro_psyir/README.md
index 602058759d..8ec34eec36 100644
--- a/tutorial/practicals/generic/1_intro_psyir/README.md
+++ b/tutorial/practicals/generic/1_intro_psyir/README.md
@@ -166,7 +166,7 @@ content of the program (the sequence of executable statements) as children.
 ## 3. Interpreting the PSyIR ##
 
 The basic structure and means of navigating the PSyIR are covered in the
-[PSyIR - Tree navigation documentation](https://psyclone.readthedocs.io/en/latest/psyir.html#tree-navigation).
+[PSyIR - Tree navigation documentation](https://psyclone.readthedocs.io/en/latest/user_guide/psyir.html#tree-navigation).
 In summary, all nodes in the PSyIR have `parent` and `children`
 properties and a `walk` method which may be used to find all nodes of
 a given type (or types) below the current node. Various sub-classes of

From 6b881b03a779392051f4589a0f327338f0022ffe Mon Sep 17 00:00:00 2001
From: Sergi Siso <sergiesg@gmail.com>
Date: Mon, 21 Jul 2025 11:42:41 +0100
Subject: [PATCH 07/11] #3058 Fix more links

---
 examples/gocean/eg5/value_range_check/README.md | 2 +-
 examples/lfric/eg14/README.md                   | 3 ++-
 lib/extract/ascii/generic/README.md             | 4 ++--
 lib/extract/binary/lfric/README.md              | 2 +-
 lib/extract/netcdf/README.md                    | 6 +++---
 lib/extract/netcdf/lfric/README.md              | 2 +-
 lib/profiling/lfric_timer/README.md             | 2 +-
 lib/read_only/README.md                         | 6 +++---
 lib/read_only/dl_esm_inf/README.md              | 8 ++++----
 lib/read_only/generic/README.md                 | 6 +++---
 lib/read_only/lfric/README.md                   | 8 ++++----
 lib/value_range_check/README.md                 | 6 +++---
 lib/value_range_check/dl_esm_inf/README.md      | 8 ++++----
 lib/value_range_check/lfric/README.md           | 8 ++++----
 14 files changed, 36 insertions(+), 35 deletions(-)

diff --git a/examples/gocean/eg5/value_range_check/README.md b/examples/gocean/eg5/value_range_check/README.md
index fb020947e2..5b34894ac9 100644
--- a/examples/gocean/eg5/value_range_check/README.md
+++ b/examples/gocean/eg5/value_range_check/README.md
@@ -29,7 +29,7 @@ invalid numbers (Infinity).
 ## Running
 In order to activate the value range checking, you need to
 specify the value range for variables as outlined here:
-https://psyclone.readthedocs.io/en/latest/psy_data.html#value-range-check
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html#value-range-check
 
 ```
 $ PSYVERIFY__main__init__b_fld=2:3    ./value_range_check
diff --git a/examples/lfric/eg14/README.md b/examples/lfric/eg14/README.md
index 2937035377..49aacb08a0 100644
--- a/examples/lfric/eg14/README.md
+++ b/examples/lfric/eg14/README.md
@@ -6,7 +6,8 @@ more detail in the directory
 ``<PSYCLONEHOME>/examples/lfric/eg17/full_example``.
 
 The script ``acc_parallel.py`` applies various OpenACC transformations
-to all kernels. See the PSyclone User Guide for [details](https://psyclone.readthedocs.io/en/stable/examples.html#example-14-openacc).
+to all kernels. See the PSyclone User Guide for [details](
+https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/lfric_examples.html#example-14-openacc).
 
 ## Compilation
 
diff --git a/lib/extract/ascii/generic/README.md b/lib/extract/ascii/generic/README.md
index 1f5f8f59c2..038afe5e17 100644
--- a/lib/extract/ascii/generic/README.md
+++ b/lib/extract/ascii/generic/README.md
@@ -8,8 +8,8 @@ A stand-alone driver can then be used to rerun this specific code region and
 verify the results (or compare performance).
 
 A full, stand-alone and runnable example can be found in
-[``examples/nemo/eg7/``](
-https://github.com/stfc/PSyclone/tree/master/examples/nemo/eg7).
+[``examples/nemo/eg5/``](
+https://github.com/stfc/PSyclone/tree/master/examples/nemo/eg5).
 
 ## Dependencies
 
diff --git a/lib/extract/binary/lfric/README.md b/lib/extract/binary/lfric/README.md
index fd80ec5f04..f92af16e5d 100644
--- a/lib/extract/binary/lfric/README.md
+++ b/lib/extract/binary/lfric/README.md
@@ -23,7 +23,7 @@ the application. The following dependencies must be available:
   https://github.com/stfc/PSyclone/tree/master/examples/lfric/eg17), however
   it is not included in the PSyclone [installation](
   ./../../../README.md#installation). See the [LFRic API](
-  https://psyclone.readthedocs.io/en/latest/lfric.html) documentation
+  https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html) documentation
   for information on how to obtain access to the LFRic code.
 
 - The ExtractBinary (``extract_binary_base.jinja``) and PSyData
diff --git a/lib/extract/netcdf/README.md b/lib/extract/netcdf/README.md
index ee38d3b8c1..12e6e959c5 100644
--- a/lib/extract/netcdf/README.md
+++ b/lib/extract/netcdf/README.md
@@ -1,9 +1,9 @@
 # Kernel Extraction Library Using NetCDF
 
 This directory contains files related to [writing (extracting)](
-https://psyclone.readthedocs.io/en/stable/psyke.html) input and output
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html) input and output
 parameters of instrumented code regions to a [NetCDF file](
-https://psyclone.readthedocs.io/en/stable/psyke.html#netcdf-extraction-example).
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#netcdf-extraction-example).
 There is a [PSyData base class](
 https://psyclone.readthedocs.io/en/latest/developer_guide/psy_data.html#psydata-base-class)
 as a Jinja template that can be used to simplify the creation of API-specific
@@ -40,7 +40,7 @@ Contains the NetCDF-extract, PSyData-API-based, wrapper library for the
 
 Contains the NetCDF-extract, PSyData-API-based, wrapper library for the
 [LFRic API](
-https://psyclone.readthedocs.io/en/latest/lfric.html).
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html).
 
 <!--
 ## Licence
diff --git a/lib/extract/netcdf/lfric/README.md b/lib/extract/netcdf/lfric/README.md
index 5e72f3687d..2fb684f919 100644
--- a/lib/extract/netcdf/lfric/README.md
+++ b/lib/extract/netcdf/lfric/README.md
@@ -20,7 +20,7 @@ the application. The following dependencies must be available:
   https://github.com/stfc/PSyclone/tree/master/examples/lfric/eg17), however
   it is not included in the PSyclone [installation](
   ./../../../README.md#installation). See the [LFRic API](
-  https://psyclone.readthedocs.io/en/latest/lfric.html) documentation
+  https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html) documentation
   for information on how to obtain access to the LFRic code.
 
 - This library uses NetCDF to store the data, so NetCDF must
diff --git a/lib/profiling/lfric_timer/README.md b/lib/profiling/lfric_timer/README.md
index 699d0f8795..10206d94cd 100644
--- a/lib/profiling/lfric_timer/README.md
+++ b/lib/profiling/lfric_timer/README.md
@@ -4,7 +4,7 @@ This is a wrapper library that maps PSyclone's [PSyData](
 https://psyclone.readthedocs.io/en/stable/psy_data.html) [profiling API](
 https://psyclone.readthedocs.io/en/stable/profiling.html#profiling) to the
 timer functionality provided in LFRic (see the [LFRic API](
-https://psyclone.readthedocs.io/en/latest/lfric.html) documentation
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html) documentation
 on how to access and use the LFRic code).
 
 ## Dependencies
diff --git a/lib/read_only/README.md b/lib/read_only/README.md
index 4367e69ebb..f3171fdc03 100644
--- a/lib/read_only/README.md
+++ b/lib/read_only/README.md
@@ -1,7 +1,7 @@
 # Read-Only Verification Libraries
 
 This directory contains files related to [read-only verification](
-https://psyclone.readthedocs.io/en/latest/psy_data.html#read-only-verification),
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html#read-only-verification),
 i.e. checks at runtime that a read-only parameter of a subroutine is indeed
 not changed in a kernel. There is a
 [PSyData read-only verification base class](
@@ -30,13 +30,13 @@ this directory.
 
 Contains the read-only, PSyData-API-based, wrapper library for the
 ``dl_esm_inf`` [GOcean API](
-https://psyclone.readthedocs.io/en/latest/gocean1p0.html).
+https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html).
 
 ## [``lfric``](./lfric) directory
 
 Contains the read-only, PSyData-API-based, wrapper library for the
 [LFRic API](
-https://psyclone.readthedocs.io/en/latest/lfric.html).
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html).
 
 ## [``generic``](./generic) directory
 
diff --git a/lib/read_only/dl_esm_inf/README.md b/lib/read_only/dl_esm_inf/README.md
index d448248c2a..b4e836857e 100644
--- a/lib/read_only/dl_esm_inf/README.md
+++ b/lib/read_only/dl_esm_inf/README.md
@@ -1,7 +1,7 @@
 # Read-only Verification Library for GOcean
 
 This library implements the [PSyData API](
-https://psyclone.readthedocs.io/en/latest/psy_data.html#read-only-verification-library-for-gocean)
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html#read-only-verification-library-for-gocean)
 to verify that variables declared read-only are not modified (overwritten) in
 a kernel call for an application using the [``dl_esm_inf`` library](
 https://github.com/stfc/dl_esm_inf).
@@ -12,10 +12,10 @@ https://github.com/stfc/PSyclone/tree/master/examples/gocean/eg5/readonly).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface
 with the application. The following dependencies must be available:
 
-- The [GOcean](https://psyclone.readthedocs.io/en/latest/gocean1p0.html)
+- The [GOcean](https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html)
   infrastructure library ``dl_esm_inf``. A stable version of this is included
   in the PSyclone repository as a Git submodule (see ["Installation"](
   https://psyclone.readthedocs.io/en/latest/developer_guide/working_practises.html#dev-installation)
@@ -60,7 +60,7 @@ The ``Makefile`` will compile the ``dl_esm_inf`` infrastructure library,
 ``lib_fd.a``, if required, with the previously selected compiler flags.
 
 Similar to compilation of the [examples](
-https://psyclone.readthedocs.io/en/latest/tutorials_and_examples.html#compilation), the
+https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/examples_intro.html#compilation), the
 compiled wrapper library can be removed by running ``make clean``. To also
 remove the compiled infrastructure library it is necessary to run
 ``make allclean`` (this is especially important if changing compilers
diff --git a/lib/read_only/generic/README.md b/lib/read_only/generic/README.md
index d67056518f..2e6c056232 100644
--- a/lib/read_only/generic/README.md
+++ b/lib/read_only/generic/README.md
@@ -1,7 +1,7 @@
 # Read-only Verification Library for Generic Fortran Code
 
 This library implements the [PSyData API](
-https://psyclone.readthedocs.io/en/latest/psy_data.html#read-only-verification-library-for-generic-fortran)
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html#read-only-verification-library-for-generic-fortran)
 to verify that variables declared read-only are not modified (overwritten) in
 a kernel.
 
@@ -11,7 +11,7 @@ https://github.com/stfc/PSyclone/tree/master/examples/nemo/eg6).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface
 with the application. It needs the ReadOnly (``read_only_base.jinja``) and
 PSyData (``psy_data_base.jinja``) base classes, which are included in PSyclone
 installation. These Jinja templates are processed to create
@@ -36,7 +36,7 @@ respectively. They default to the relative paths to the
 The compilation process will create the wrapper library ``lib_read_only.a``.
 
 Similar to compilation of the [examples](
-https://psyclone.readthedocs.io/en/latest/tutorials_and_examples.html#compilation), the
+https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/examples_intro.html#compilation), the
 compiled wrapper library can be removed by running ``make clean``. 
 
 ### Linking the wrapper library
diff --git a/lib/read_only/lfric/README.md b/lib/read_only/lfric/README.md
index dce8961d5a..efe9c46e7c 100644
--- a/lib/read_only/lfric/README.md
+++ b/lib/read_only/lfric/README.md
@@ -1,14 +1,14 @@
 # Read-only Verification Library for LFRic
 
 This library implements the [PSyData API](
-https://psyclone.readthedocs.io/en/latest/psy_data.html#read-only-verification-library-for-lfric)
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html#read-only-verification-library-for-lfric)
 to verify that variables declared read-only are not modified (overwritten) in
 a kernel call for an application using the LFRic infrastructure library.
 
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The LFRic infrastructure library. A pared-down version of LFRic
@@ -17,7 +17,7 @@ the application. The following dependencies must be available:
   https://github.com/stfc/PSyclone/tree/master/examples/lfric/eg17), however
   it is not included in the PSyclone [installation](
   ./../../README.md#installation). See the [LFRic API](
-  https://psyclone.readthedocs.io/en/latest/lfric.html) documentation
+  https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html) documentation
   for information on how to obtain access to the LFRic code.
 
 - The ReadOnly (``read_only_base.jinja``) and PSyData
@@ -63,7 +63,7 @@ The ``Makefile`` will compile the LFRic infrastructure library,
 ``liblfric.a``, if required, with the previously selected compiler flags.
 
 Similar to compilation of the [examples](
-https://psyclone.readthedocs.io/en/latest/tutorials_and_examples.html#compilation), the
+https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/examples_intro.html#compilation), the
 compiled wrapper library can be removed by running ``make clean``. To also
 remove the compiled infrastructure library it is necessary to run
 ``make allclean`` (this is especially important if changing compilers
diff --git a/lib/value_range_check/README.md b/lib/value_range_check/README.md
index 997d2284df..641d00e1f9 100644
--- a/lib/value_range_check/README.md
+++ b/lib/value_range_check/README.md
@@ -3,7 +3,7 @@
 This directory contains files related to testing all input and output
 parameters of a kernel to make sure they are within a user-specified range,
 and not [``NaN`` or infinite](
-https://psyclone.readthedocs.io/en/latest/psy_data.html#psydata-value-range-check).
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html#psydata-value-range-check).
 
 There is a [PSyData base class](
 https://psyclone.readthedocs.io/en/latest/developer_guide/psy_data.html#psydata-base-class)
@@ -32,13 +32,13 @@ this directory.
 
 Contains the ``ValueRangeCheck``, PSyData-API-based, wrapper library for the
 ``dl_esm_inf`` [GOcean API](
-https://psyclone.readthedocs.io/en/latest/gocean1p0.html).
+https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html).
 
 ## [``lfric``](./lfric) directory
 
 Contains the ``ValueRangeCheck``, PSyData-API-based, wrapper library for the
 [LFRic API](
-https://psyclone.readthedocs.io/en/latest/lfric.html).
+https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html).
 
 <!--
 ## Licence
diff --git a/lib/value_range_check/dl_esm_inf/README.md b/lib/value_range_check/dl_esm_inf/README.md
index 16b7518aaa..dd5f634142 100644
--- a/lib/value_range_check/dl_esm_inf/README.md
+++ b/lib/value_range_check/dl_esm_inf/README.md
@@ -1,7 +1,7 @@
 # ``ValueRangeCheck`` Library for GOcean
 
 This library implements the [PSyData API](
-https://psyclone.readthedocs.io/en/latest/psy_data.html#psydata-value-range-check)
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html#psydata-value-range-check)
 to verify that input and output parameters of a GOcean kernel are within
 a user-specified range, and not ``NaN`` or infinite, using the [``dl_esm_inf`` library](
 https://github.com/stfc/dl_esm_inf).
@@ -9,10 +9,10 @@ https://github.com/stfc/dl_esm_inf).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface
 with the application. The following dependencies must be available:
 
-- The [GOcean](https://psyclone.readthedocs.io/en/latest/gocean1p0.html)
+- The [GOcean](https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html)
   infrastructure library ``dl_esm_inf``. A stable version of this is included
   in the PSyclone repository as a Git submodule (see ["Installation"](
   https://psyclone.readthedocs.io/en/latest/developer_guide/working_practises.html#dev-installation)
@@ -57,7 +57,7 @@ The ``Makefile`` will compile the ``dl_esm_inf`` infrastructure library,
 ``lib_fd.a``, if required, with the previously selected compiler flags.
 
 Similar to compilation of the [examples](
-https://psyclone.readthedocs.io/en/latest/tutorials_and_examples.html#compilation), the
+https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/examples_intro.html#compilation), the
 compiled wrapper library can be removed by running ``make clean``. To also
 remove the compiled infrastructure library it is necessary to run
 ``make allclean`` (this is especially important if changing compilers
diff --git a/lib/value_range_check/lfric/README.md b/lib/value_range_check/lfric/README.md
index 1ef6a01463..2263a950d3 100644
--- a/lib/value_range_check/lfric/README.md
+++ b/lib/value_range_check/lfric/README.md
@@ -1,7 +1,7 @@
 # ``ValueRangeCheck`` Library for LFRic
 
 This library implements the [PSyData API](
-https://psyclone.readthedocs.io/en/latest/psy_data.html#psydata-value-range-check)
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html#psydata-value-range-check)
 to verify that input and output parameters of an LFRic kernel are within
 a user-specified range, and not ``NaN`` or infinite, using the LFRic
 infrastructure library.
@@ -9,7 +9,7 @@ infrastructure library.
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The LFRic infrastructure library. A pared-down version of LFRic
@@ -18,7 +18,7 @@ the application. The following dependencies must be available:
   https://github.com/stfc/PSyclone/tree/master/examples/lfric/eg17), however
   it is not included in the PSyclone [installation](
   ./../../README.md#installation). See the [LFRic API](
-  https://psyclone.readthedocs.io/en/latest/lfric.html) documentation
+  https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html) documentation
   for information on how to obtain access to the LFRic code.
 
 - The ValueRangeCheck (``value_range_check_base.jinja``) and PSyData
@@ -64,7 +64,7 @@ The ``Makefile`` will compile the LFRic infrastructure library,
 ``liblfric.a``, if required, with the previously selected compiler flags.
 
 Similar to compilation of the [examples](
-https://psyclone.readthedocs.io/en/latest/tutorials_and_examples.html#compilation), the
+https://psyclone.readthedocs.io/en/latest/tutorials_and_examples/examples_intro.html#compilation), the
 compiled wrapper library can be removed by running ``make clean``. To also
 remove the compiled infrastructure library it is necessary to run
 ``make allclean`` (this is especially important if changing compilers

From ea180cbe76fd90500e7f5ec5fdcb14254ed4fcf6 Mon Sep 17 00:00:00 2001
From: Sergi Siso <sergiesg@gmail.com>
Date: Mon, 21 Jul 2025 11:57:29 +0100
Subject: [PATCH 08/11] #3058 Update links to stable docs to latest docs

---
 examples/lfric/eg17/full_example_extract/README.md     |  4 ++--
 examples/nemo/README.md                                |  2 +-
 lib/README.md                                          | 10 +++++-----
 lib/extract/README.md                                  |  2 +-
 lib/extract/ascii/dl_esm_inf/README.md                 |  6 +++---
 lib/extract/ascii/generic/README.md                    |  6 +++---
 lib/extract/ascii/lfric/README.md                      |  8 ++++----
 lib/extract/binary/dl_esm_inf/README.md                |  6 +++---
 lib/extract/binary/generic/README.md                   |  6 +++---
 lib/extract/binary/lfric/README.md                     |  6 +++---
 lib/extract/netcdf/dl_esm_inf/README.md                |  6 +++---
 lib/extract/netcdf/generic/README.md                   |  6 +++---
 lib/extract/netcdf/lfric/README.md                     |  6 +++---
 lib/profiling/README.md                                |  6 +++---
 lib/profiling/dl_timer/README.md                       |  4 ++--
 lib/profiling/drhook/README.md                         |  4 ++--
 lib/profiling/lfric_timer/README.md                    |  4 ++--
 lib/profiling/nvidia/README.md                         |  2 +-
 lib/profiling/simple_timing/README.md                  |  9 ++++-----
 lib/profiling/tau/README.md                            |  4 ++--
 lib/profiling/template/README.md                       |  9 ++++-----
 lib/profiling/vernier/README.md                        |  4 ++--
 lib/value_range_check/README.md                        |  2 +-
 src/psyclone/domain/gocean/kernel/psyir.py             |  7 ++-----
 .../tests/domain/nemo/test_files/nemo_test.cfg         |  2 +-
 .../1_simple_kernels/LFRic_kernel_structure.md         |  2 +-
 .../building_code/1_simple_kernels/part1/README.md     |  4 ++--
 .../building_code/1_simple_kernels/part2/README.md     |  4 ++--
 .../LFRic/building_code/2_built_ins/README.md          |  2 +-
 .../practicals/LFRic/building_code/4_psydata/README.md |  4 ++--
 tutorial/practicals/LFRic/building_code/README.md      |  4 ++--
 .../distributed_memory/2_annexed_dofs/psyclone.cfg     |  2 +-
 .../3_overlapping_comms/psyclone.cfg                   |  2 +-
 .../practicals/LFRic/single_node/1_openmp/psyclone.cfg |  2 +-
 34 files changed, 76 insertions(+), 81 deletions(-)

diff --git a/examples/lfric/eg17/full_example_extract/README.md b/examples/lfric/eg17/full_example_extract/README.md
index b65bb18c12..853d01b583 100644
--- a/examples/lfric/eg17/full_example_extract/README.md
+++ b/examples/lfric/eg17/full_example_extract/README.md
@@ -7,14 +7,14 @@ directory ``../full_example``.
 This example applies the PSyData extraction transformations to the
 two invoke statements, the first initialising two fields, the second
 doing some computations.
-See the [PSyKE](https://psyclone.readthedocs.io/en/stable/psyke.html)
+See the [PSyKE](https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html)
 chapter of the PSyclone documentation for details about this transformation.
 
 ## Compilation
 
 A simple makefile is provided to compile the example. It can use one of
 three extraction libraries, as outlined in the
-[PSyKE extraction libraries](https://psyclone.readthedocs.io/en/stable/psyke.html#extraction-libraries) section.
+[PSyKE extraction libraries](https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction-libraries) section.
 
 By default, the stand-alone binary version will be used,
 but you can set the ``TYPE`` environment variable to either ``ascii``
diff --git a/examples/nemo/README.md b/examples/nemo/README.md
index aac0847d84..1a750f0603 100644
--- a/examples/nemo/README.md
+++ b/examples/nemo/README.md
@@ -55,7 +55,7 @@ Contains:
 ## Scripts
 
 Contains the scripts used to process the NEMO code base and to add profiling
-instrumentation (https://psyclone.readthedocs.io/en/stable/profiling.html)
+instrumentation (https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html)
 and OpenACC or OpenMP directives:
 
 1. `process_nemo.py` is a driver script that allows the user to specify
diff --git a/lib/README.md b/lib/README.md
index 2b6108bb78..31b8a71d0b 100644
--- a/lib/README.md
+++ b/lib/README.md
@@ -1,7 +1,7 @@
 # Wrapper Libraries for Use with PSyclone
 
 This directory contains [PSyData-API-based](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) wrapper libraries.
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) wrapper libraries.
 They enable PSyclone to provide transformations that will insert callbacks
 to an external library at runtime. These callbacks allow third-party libraries
 to access data structures at specified locations in the code for different
@@ -13,11 +13,11 @@ The wrapper libraries for the supported use cases are listed
 
 Wrapper libraries can be accessed from a clone of PSyclone repository
 or a PSyclone [installation](
-https://psyclone.readthedocs.io/en/stable/getting_going.html). In a
+https://psyclone.readthedocs.io/en/latest/user_guide/getting_going.html). In a
 PSyclone installation the libraries may be found in ``share/psyclone/lib``
 under your Python (or PSyclone, depending on the ``pip install`` options)
 installation, see ["Getting Going"](
-https://psyclone.readthedocs.io/en/stable/getting_going.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/getting_going.html)
 for possible locations.
 
 If working with wrapper libraries from a PSyclone installation, it
@@ -32,7 +32,7 @@ dependencies, see [below](#compilation) for more information.
 
 The file ``psy_data_base.jinja`` contains a Jinja template that can be used
 by the [PSyData-API-based](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) wrapper libraries.
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) wrapper libraries.
 Full documentation on using this template is provided in the PSyclone
 [Developer Guide](
 https://psyclone.readthedocs.io/en/latest/developer_guide/psy_data.html#jinja). The
@@ -115,7 +115,7 @@ libraries are compiled in a clone of PSyclone repository or in a PSyclone
 Compilation of ``extract``, ``nan_test``, ``read_only`` and some of the
 profiling wrapper libraries depends on infrastructure libraries relevant
 to the API they are used for. [GOcean API](
-https://psyclone.readthedocs.io/en/stable/gocean1p0.html) uses the
+https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html) uses the
 [``dl_esm_inf`` library](https://github.com/stfc/dl_esm_inf) and
 [LFRic API](
 https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html)
diff --git a/lib/extract/README.md b/lib/extract/README.md
index 4b14a0f933..c12a603e8c 100755
--- a/lib/extract/README.md
+++ b/lib/extract/README.md
@@ -1,7 +1,7 @@
 # Kernel Extraction Library
 
 This directory contains files related to [writing (extracting)](
-https://psyclone.readthedocs.io/en/stable/psyke.html) input and output
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html) input and output
 parameters of instrumented code regions.
 
 For now the parameter extraction is only implemented to write out the
diff --git a/lib/extract/ascii/dl_esm_inf/README.md b/lib/extract/ascii/dl_esm_inf/README.md
index 14c7d3585e..7544b2d385 100644
--- a/lib/extract/ascii/dl_esm_inf/README.md
+++ b/lib/extract/ascii/dl_esm_inf/README.md
@@ -1,9 +1,9 @@
 # Stand-alone ASCII Kernel Extraction Library for GOcean
 
 This wrapper library is used to [write (extract)](
-https://psyclone.readthedocs.io/en/stable/psyke.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html)
 input and output parameters of instrumented code regions to an [ASCII file](
-https://psyclone.readthedocs.io/en/stable/psyke.html#extraction_libraries)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction_libraries)
 using the [``dl_esm_inf`` library](https://github.com/stfc/dl_esm_inf).
 A stand-alone driver can then be used to rerun this specific code region and
 verify the results (or compare performance). This version of the extraction
@@ -19,7 +19,7 @@ https://github.com/stfc/PSyclone/tree/master/examples/gocean/eg5/extract).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The [GOcean](https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html)
diff --git a/lib/extract/ascii/generic/README.md b/lib/extract/ascii/generic/README.md
index 038afe5e17..3de7a91efb 100644
--- a/lib/extract/ascii/generic/README.md
+++ b/lib/extract/ascii/generic/README.md
@@ -1,9 +1,9 @@
 # Stand-alone Kernel Extraction Library for generic Fortran code
 
 This wrapper library is used to [write (extract)](
-https://psyclone.readthedocs.io/en/stable/psyke.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html)
 input and output parameters of instrumented code regions to an [ASCII file](
-https://psyclone.readthedocs.io/en/stable/psyke.html#extraction_libraries).
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction_libraries).
 A stand-alone driver can then be used to rerun this specific code region and
 verify the results (or compare performance).
 
@@ -14,7 +14,7 @@ https://github.com/stfc/PSyclone/tree/master/examples/nemo/eg5).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The ExtractAsciiBase (``extract_ascii_base.jinja``)
diff --git a/lib/extract/ascii/lfric/README.md b/lib/extract/ascii/lfric/README.md
index fd52fe1cab..6386aaf1a1 100644
--- a/lib/extract/ascii/lfric/README.md
+++ b/lib/extract/ascii/lfric/README.md
@@ -1,9 +1,9 @@
 # Kernel Extraction Library for LFRic
 
 This wrapper library [writes (extracts)](
-https://psyclone.readthedocs.io/en/stable/psyke.html) input and output
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html) input and output
 parameters of instrumented code regions to a stand-alone
-[binary file](https://psyclone.readthedocs.io/en/stable/psyke.html#extraction_libraries)
+[binary file](https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction_libraries)
 using the LFRic infrastructure library. A stand-alone driver can then be
 used to rerun this specific code region and verify the results (or
 compare performance).
@@ -11,7 +11,7 @@ compare performance).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The LFRic infrastructure library. A pared-down version of LFRic
@@ -20,7 +20,7 @@ the application. The following dependencies must be available:
   https://github.com/stfc/PSyclone/tree/master/examples/lfric/eg17), however
   it is not included in the PSyclone [installation](
   ./../../../README.md#installation). See the [LFRic API](
-  https://psyclone.readthedocs.io/en/stable/dynamo0p3.html) documentation
+  https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html) documentation
   for information on how to obtain access to the LFRic code.
 
 - The ExtractAsciiBase (``extract_ascii_base.jinja``) and PSyData
diff --git a/lib/extract/binary/dl_esm_inf/README.md b/lib/extract/binary/dl_esm_inf/README.md
index c81ae04622..82f8805111 100644
--- a/lib/extract/binary/dl_esm_inf/README.md
+++ b/lib/extract/binary/dl_esm_inf/README.md
@@ -1,9 +1,9 @@
 # Stand-alone Kernel Extraction Library for GOcean
 
 This wrapper library is used to [write (extract)](
-https://psyclone.readthedocs.io/en/stable/psyke.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html)
 input and output parameters of instrumented code regions to a [binary file](
-https://psyclone.readthedocs.io/en/stable/psyke.html#extraction_libraries)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction_libraries)
 using the [``dl_esm_inf`` library](https://github.com/stfc/dl_esm_inf).
 A stand-alone driver can then be used to rerun this specific code region and
 verify the results (or compare performance).
@@ -15,7 +15,7 @@ https://github.com/stfc/PSyclone/tree/master/examples/gocean/eg5/extract).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The [GOcean](https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html)
diff --git a/lib/extract/binary/generic/README.md b/lib/extract/binary/generic/README.md
index 4751f9c910..0d77bed0ff 100644
--- a/lib/extract/binary/generic/README.md
+++ b/lib/extract/binary/generic/README.md
@@ -1,9 +1,9 @@
 # Stand-alone Kernel Extraction Library for generic Fortran code
 
 This wrapper library is used to [write (extract)](
-https://psyclone.readthedocs.io/en/stable/psyke.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html)
 input and output parameters of instrumented code regions to a [binary file](
-https://psyclone.readthedocs.io/en/stable/psyke.html#extraction_libraries).
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction_libraries).
 A stand-alone driver can then be used to rerun this specific code region and
 verify the results (or compare performance).
 
@@ -14,7 +14,7 @@ https://github.com/stfc/PSyclone/tree/master/examples/nemo/eg5).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The ExtractBinary (``extract_binary_base.jinja``) and PSyData
diff --git a/lib/extract/binary/lfric/README.md b/lib/extract/binary/lfric/README.md
index f92af16e5d..bd010733d0 100644
--- a/lib/extract/binary/lfric/README.md
+++ b/lib/extract/binary/lfric/README.md
@@ -1,9 +1,9 @@
 # Kernel Extraction Library for LFRic
 
 This wrapper library [writes (extracts)](
-https://psyclone.readthedocs.io/en/stable/psyke.html) input and output
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html) input and output
 parameters of instrumented code regions to a stand-alone
-[binary file](https://psyclone.readthedocs.io/en/stable/psyke.html#extraction_libraries)
+[binary file](https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#extraction_libraries)
 using the LFRic infrastructure library. A stand-alone driver can then be
 used to rerun this specific code region and verify the results (or
 compare performance).
@@ -14,7 +14,7 @@ compilation tests.
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The LFRic infrastructure library. A pared-down version of LFRic
diff --git a/lib/extract/netcdf/dl_esm_inf/README.md b/lib/extract/netcdf/dl_esm_inf/README.md
index 5345e9faf9..eab951a29a 100644
--- a/lib/extract/netcdf/dl_esm_inf/README.md
+++ b/lib/extract/netcdf/dl_esm_inf/README.md
@@ -1,9 +1,9 @@
 # Kernel Extraction Library Using NetCDF for GOcean
 
 This wrapper library is used to [write (extract)](
-https://psyclone.readthedocs.io/en/stable/psyke.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html)
 input and output parameters of instrumented code regions to a [NetCDF file](
-https://psyclone.readthedocs.io/en/stable/psyke.html#netcdf-extraction-example)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#netcdf-extraction-example)
 using the [``dl_esm_inf`` library](https://github.com/stfc/dl_esm_inf).
 A stand-alone driver can then be used to rerun this specific code region and
 verify the results (or compare performance).
@@ -15,7 +15,7 @@ https://github.com/stfc/PSyclone/tree/master/examples/gocean/eg5/extract).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The [GOcean](https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html)
diff --git a/lib/extract/netcdf/generic/README.md b/lib/extract/netcdf/generic/README.md
index a3a3b3c154..e6e0826ff9 100644
--- a/lib/extract/netcdf/generic/README.md
+++ b/lib/extract/netcdf/generic/README.md
@@ -1,9 +1,9 @@
 # Kernel Extraction Library Using NetCDF for generic Fortran code
 
 This wrapper library is used to [write (extract)](
-https://psyclone.readthedocs.io/en/stable/psyke.html)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html)
 input and output parameters of instrumented code regions to a [NetCDF file](
-https://psyclone.readthedocs.io/en/stable/psyke.html#netcdf-extraction-example).
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#netcdf-extraction-example).
 A stand-alone driver can then be used to rerun this specific code region and
 verify the results (or compare performance).
 
@@ -14,7 +14,7 @@ https://github.com/stfc/PSyclone/tree/master/examples/nemo/eg5).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - This library uses NetCDF to store the data, so NetCDF must
diff --git a/lib/extract/netcdf/lfric/README.md b/lib/extract/netcdf/lfric/README.md
index 2fb684f919..aab17a76af 100644
--- a/lib/extract/netcdf/lfric/README.md
+++ b/lib/extract/netcdf/lfric/README.md
@@ -1,9 +1,9 @@
 # Kernel Extraction Library Using NetCDF for LFRic
 
 This wrapper library [writes (extracts)](
-https://psyclone.readthedocs.io/en/stable/psyke.html) input and output
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html) input and output
 parameters of instrumented code regions to a [NetCDF file](
-https://psyclone.readthedocs.io/en/stable/psyke.html#netcdf-extraction-example)
+https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#netcdf-extraction-example)
 using the LFRic infrastructure library. A stand-alone driver can then be
 used to rerun this specific code region and verify the results (or
 compare performance).
@@ -11,7 +11,7 @@ compare performance).
 ## Dependencies
 
 This library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The following dependencies must be available:
 
 - The LFRic infrastructure library. A pared-down version of LFRic
diff --git a/lib/profiling/README.md b/lib/profiling/README.md
index 367173566f..0a78b6b93e 100644
--- a/lib/profiling/README.md
+++ b/lib/profiling/README.md
@@ -2,9 +2,9 @@
 
 This directory contains wrapper libraries that can be used with [PSyclone
 profiling API](
-https://psyclone.readthedocs.io/en/stable/profiling.html#profiling). All
+https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html#profiling). All
 profiling-library interfaces use the the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html). The profiling
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html). The profiling
 wrappers included in PSyclone are: ``template``,
 ``simple_timing``, ``dl_timer``, ``drhook``, ``nvidia``, ``tau`` and
 ``lfric_timer``. The overview is given below (for more information please
@@ -50,7 +50,7 @@ Example output:
 ### [``dl_timer``](./dl_timer)
 
 This is a wrapper library that maps the [PSyclone profiling API](
-https://psyclone.readthedocs.io/en/stable/profiling.html#profiling) to the
+https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html#profiling) to the
 dl_timer API. A copy of dl_timer can be downloaded from
 https://bitbucket.org/apeg/dl_timer.
 
diff --git a/lib/profiling/dl_timer/README.md b/lib/profiling/dl_timer/README.md
index f0a685ab9d..30c415f103 100644
--- a/lib/profiling/dl_timer/README.md
+++ b/lib/profiling/dl_timer/README.md
@@ -1,7 +1,7 @@
 # PSyclone Wrapper Library for ``dl_timer``
 
 This is a wrapper library that maps the [PSyclone profiling API](
-https://psyclone.readthedocs.io/en/stable/profiling.html#profiling) to the
+https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html#profiling) to the
 dl_timer API. This library is **thread-safe**.
 
 ## Dependencies
@@ -10,7 +10,7 @@ The library dl_timer must be installed, which can be downloaded from
 https://bitbucket.org/apeg/dl_timer.
 
 This profiling library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The library is based on the [PSyData base class](
 https://psyclone.readthedocs.io/en/latest/developer_guide/psy_data.html#psydata-base-class),
 which is included in PSyclone as a Jinja template, ``psy_data_base.jinja``.
diff --git a/lib/profiling/drhook/README.md b/lib/profiling/drhook/README.md
index f85f93fbc5..8b43ce1437 100644
--- a/lib/profiling/drhook/README.md
+++ b/lib/profiling/drhook/README.md
@@ -1,7 +1,7 @@
 # PSyclone Wrapper Library for Dr Hook
 
 This is a wrapper library that maps the [PSyclone profiling API](
-https://psyclone.readthedocs.io/en/stable/profiling.html#profiling)
+https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html#profiling)
 to the Dr Hook API.
 
 ## Dependencies
@@ -11,7 +11,7 @@ not available on any public repository and the prospective user needs
 to contact ECMWF to obtain a copy of Dr Hook.
 
 This profiling library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The library is based on the [PSyData base class](
 https://psyclone.readthedocs.io/en/latest/developer_guide/psy_data.html#psydata-base-class),
 which is included in PSyclone as a Jinja template, ``psy_data_base.jinja``.
diff --git a/lib/profiling/lfric_timer/README.md b/lib/profiling/lfric_timer/README.md
index 10206d94cd..f776fe4448 100644
--- a/lib/profiling/lfric_timer/README.md
+++ b/lib/profiling/lfric_timer/README.md
@@ -1,8 +1,8 @@
 # PSyclone Wrapper Library for LFRic
 
 This is a wrapper library that maps PSyclone's [PSyData](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) [profiling API](
-https://psyclone.readthedocs.io/en/stable/profiling.html#profiling) to the
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) [profiling API](
+https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html#profiling) to the
 timer functionality provided in LFRic (see the [LFRic API](
 https://psyclone.readthedocs.io/en/latest/user_guide/lfric.html) documentation
 on how to access and use the LFRic code).
diff --git a/lib/profiling/nvidia/README.md b/lib/profiling/nvidia/README.md
index 8cd925ab66..e056f8b83d 100644
--- a/lib/profiling/nvidia/README.md
+++ b/lib/profiling/nvidia/README.md
@@ -1,7 +1,7 @@
 # NVTX Wrapper
 
 This is a wrapper library that maps the [PSyclone profiling API](
-https://psyclone.readthedocs.io/en/stable/profiling.html#profiling) to the
+https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html#profiling) to the
 NVIDIA Tools Extension library (NVTX). Unlike some of the other
 profiling tools, the use of this library does *not* require that calls
 to ``profile_PSyDataInit()`` and ``profile_PSyDataShutdown()`` be inserted
diff --git a/lib/profiling/simple_timing/README.md b/lib/profiling/simple_timing/README.md
index 8e2be7f12d..6de0840535 100644
--- a/lib/profiling/simple_timing/README.md
+++ b/lib/profiling/simple_timing/README.md
@@ -1,9 +1,8 @@
 # Simple Stand-alone Timer Library
 
-This library is a simple stand-alone timer library (see the ["Profiling"](
-https://psyclone.readthedocs.io/en/stable/profiling.html#profiling) section
-in the PSyclone [User Guide](https://psyclone.readthedocs.io/en/stable/) for
-more details). It counts the number of calls for each region, and reports
+This library is a simple stand-alone timer library (see the [User Guide Profiling](
+https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html#profiling) section
+for more details). It counts the number of calls for each region, and reports
 minumum, maximum and average times. This library is **not thread-safe**, and
 **not MPI-aware** (e.g. maximum reported is per process, not across all
 processes).
@@ -11,7 +10,7 @@ processes).
 ## Dependencies
 
 This stand-alone profiling library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The library is based on the [PSyData base class](
 https://psyclone.readthedocs.io/en/latest/developer_guide/psy_data.html#psydata-base-class),
 which is included in PSyclone as a Jinja template, ``psy_data_base.jinja``.
diff --git a/lib/profiling/tau/README.md b/lib/profiling/tau/README.md
index d0c3f46ba2..ece9fe8830 100644
--- a/lib/profiling/tau/README.md
+++ b/lib/profiling/tau/README.md
@@ -1,7 +1,7 @@
 # PSyclone Wrapper Library for TAU
 
 This is a wrapper library that maps the [PSyclone profiling API](
-https://psyclone.readthedocs.io/en/stable/profiling.html#profiling)
+https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html#profiling)
 to the TAU API.
 
 ## Dependencies
@@ -10,7 +10,7 @@ TAU must be available at link time but is not actually required when compiling t
 PSyData wrapper.
 
 This profiling library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The library is based on the [PSyData base class](
 https://psyclone.readthedocs.io/en/latest/developer_guide/psy_data.html#psydata-base-class),
 which is included in PSyclone as a Jinja template, ``psy_data_base.jinja``.
diff --git a/lib/profiling/template/README.md b/lib/profiling/template/README.md
index 5c9006a329..28e28bd380 100644
--- a/lib/profiling/template/README.md
+++ b/lib/profiling/template/README.md
@@ -1,11 +1,10 @@
 # PSyclone Wrapper Library Template
 
 This is a simple example to help writing your own PSyclone [PSyData-API-based](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) profile library (see
-the ["Profiling"](
-https://psyclone.readthedocs.io/en/stable/profiling.html#profiling) section
-in the PSyclone [User Guide](https://psyclone.readthedocs.io/en/stable/) for
-more information). It only prints out the function called at runtime and does
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) profile library (see
+the [User Guide Profiling](
+https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html#profiling) section
+for more information). It only prints out the function called at runtime and does
 not do any actual measurements.
 
 ## Dependencies
diff --git a/lib/profiling/vernier/README.md b/lib/profiling/vernier/README.md
index 6cc5d0522f..5df9d126b4 100644
--- a/lib/profiling/vernier/README.md
+++ b/lib/profiling/vernier/README.md
@@ -1,7 +1,7 @@
 # PSyclone Wrapper Library for Vernier
 
 This is a wrapper library that maps the [PSyclone profiling API](
-https://psyclone.readthedocs.io/en/stable/profiling.html#profiling)
+https://psyclone.readthedocs.io/en/latest/user_guide/profiling.html#profiling)
 to [Vernier](https://github.com/MetOffice/Vernier).
 
 ## Dependencies
@@ -9,7 +9,7 @@ to [Vernier](https://github.com/MetOffice/Vernier).
 Vernier  must be installed.
 
 This profiling library uses the [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) to interface with
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) to interface with
 the application. The library is based on the [PSyData base class](
 https://psyclone.readthedocs.io/en/latest/developer_guide/psy_data.html#psydata-base-class),
 which is included in PSyclone as a Jinja template, ``psy_data_base.jinja``.
diff --git a/lib/value_range_check/README.md b/lib/value_range_check/README.md
index 641d00e1f9..6581c1e57f 100644
--- a/lib/value_range_check/README.md
+++ b/lib/value_range_check/README.md
@@ -15,7 +15,7 @@ wrapper libraries.
 The file ``value_range_check_base.jinja`` contains a Jinja template that is used
 by the [GOcean ``dl_esm_inf``-](./dl_esm_inf/README.md) and [LFRic-specific](
 ./lfric/README.md) wrapper libraries. It implements the required [PSyData API](
-https://psyclone.readthedocs.io/en/stable/psy_data.html) calls for
+https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html) calls for
 Fortran base types (scalar and arrays).
 Full documentation to the Jinja implementation of a PSyData base class is
 in the PSyclone [Developer Guide](
diff --git a/src/psyclone/domain/gocean/kernel/psyir.py b/src/psyclone/domain/gocean/kernel/psyir.py
index a21837ae96..8aab5b3259 100644
--- a/src/psyclone/domain/gocean/kernel/psyir.py
+++ b/src/psyclone/domain/gocean/kernel/psyir.py
@@ -885,11 +885,8 @@ def stencil(self):
         @stencil.setter
         def stencil(self, value_list):
             '''
-            :param value_list: set the new stencil value, encoded as \
-                three strings, each of three digits (0 or 1), see the \
-                `psyclone user guide <https://psyclone.readthedocs.io/en/\
-stable/gocean1p0.html#argument-metadata-meta-args>` \
-                for more details.
+            :param value_list: set the new stencil value, encoded as
+                three strings, each of three digits (0 or 1).
             :type value_list: List[str]
 
             '''
diff --git a/src/psyclone/tests/domain/nemo/test_files/nemo_test.cfg b/src/psyclone/tests/domain/nemo/test_files/nemo_test.cfg
index d6a453a290..3b265cb6ba 100644
--- a/src/psyclone/tests/domain/nemo/test_files/nemo_test.cfg
+++ b/src/psyclone/tests/domain/nemo/test_files/nemo_test.cfg
@@ -98,7 +98,7 @@ access_mapping = go_read: read, go_write: write, go_readwrite: readwrite
 # go_grid_{internal,whole}_{inner,outer}_{start,stop}
 # Details about the grid properties and their usage can be found in the
 # PSyclone documentation at:
-# https://psyclone.readthedocs.io/en/stable/gocean1p0.html#argument-metadata-meta-args
+# https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html#argument-metadata-meta-args
 grid-properties = go_grid_xstop: {0}%%grid%%subdomain%%internal%%xstop: scalar: integer,
                   go_grid_ystop: {0}%%grid%%subdomain%%internal%%ystop: scalar: integer,
                   go_grid_data: {0}%%data: array: real,
diff --git a/tutorial/practicals/LFRic/building_code/1_simple_kernels/LFRic_kernel_structure.md b/tutorial/practicals/LFRic/building_code/1_simple_kernels/LFRic_kernel_structure.md
index 560a237145..a8b22dd820 100644
--- a/tutorial/practicals/LFRic/building_code/1_simple_kernels/LFRic_kernel_structure.md
+++ b/tutorial/practicals/LFRic/building_code/1_simple_kernels/LFRic_kernel_structure.md
@@ -146,7 +146,7 @@ object. As a rule, object data are `private` as illustrated in the
 
 ### Argument list and declarations
 
-Running the PSyclone [kernel tool](https://psyclone.readthedocs.io/en/stable/psyclone_kern.html) 
+Running the PSyclone [kernel tool](https://psyclone.readthedocs.io/en/latest/user_guide/psyclone_kern.html) 
 on `setval_field_w0_kernel_mod.f90` produces the argument list and
 declarations for the `setval_field_w0_code`, enclosed in a module:
 
diff --git a/tutorial/practicals/LFRic/building_code/1_simple_kernels/part1/README.md b/tutorial/practicals/LFRic/building_code/1_simple_kernels/part1/README.md
index 487fd8985a..44296edaac 100644
--- a/tutorial/practicals/LFRic/building_code/1_simple_kernels/part1/README.md
+++ b/tutorial/practicals/LFRic/building_code/1_simple_kernels/part1/README.md
@@ -2,7 +2,7 @@
 
 In this part of the [first tutorial](../README.md), we will use the
 [stub-generation](
-https://psyclone.readthedocs.io/en/stable/psyclone_kern.html) functionality
+https://psyclone.readthedocs.io/en/latest/user_guide/psyclone_kern.html) functionality
 of the PSyclone kernel tool to create the argument list and declarations
 for two kernels, one that assigns a value to a field on a continuous
 `W0` function space and another on a discontinuous `W3` function space.
@@ -169,7 +169,7 @@ The name of the generated `invoke` subroutine in this case is just the
 `invoke` keyword with the appended numerical index. If there was a separate
 `invoke` call for each kernel, the subroutine name would also contain the
 name of the called kernel (see [PSyclone Algorithm-layer](
-https://psyclone.readthedocs.io/en/stable/introduction_to_psykal.html#algorithm-layer)
+https://psyclone.readthedocs.io/en/latest/user_guide/introduction_to_psykal.html#algorithm-layer)
 documentation for more information).
 
 The generated `invoke_0` subroutine code is located in the generated PSy-layer
diff --git a/tutorial/practicals/LFRic/building_code/1_simple_kernels/part2/README.md b/tutorial/practicals/LFRic/building_code/1_simple_kernels/part2/README.md
index 568a73c1e3..a4c38fc59c 100644
--- a/tutorial/practicals/LFRic/building_code/1_simple_kernels/part2/README.md
+++ b/tutorial/practicals/LFRic/building_code/1_simple_kernels/part2/README.md
@@ -1,7 +1,7 @@
 # Tutorial 1, Part 2: Update fields on a generic function space
 
 In this part of the [first tutorial](../README.md), we will use the
-[stub-generation](https://psyclone.readthedocs.io/en/stable/psyclone_kern.html)
+[stub-generation](https://psyclone.readthedocs.io/en/latest/user_guide/psyclone_kern.html)
 functionality of the PSyclone kernel tool to
 create the argument list and declarations for a generic kernel that
 assigns a value to a field on any function space. For this we will use
@@ -86,7 +86,7 @@ The argument list and declarations are generated in one line per
 statement each, so in this case of long argument names they may overrun
 the free-form Fortran line-length limit of 132 characters and PSyclone
 will complain when building the code (see e.g. [here](
-https://psyclone.readthedocs.io/en/stable/line_length.html)). To wrap
+https://psyclone.readthedocs.io/en/latest/user_guide/psyclone_command.html#fortran-line-length)). To wrap
 long lines just use the `-l output` flag when running the kernel tool, e.g.
 
 ```shell
diff --git a/tutorial/practicals/LFRic/building_code/2_built_ins/README.md b/tutorial/practicals/LFRic/building_code/2_built_ins/README.md
index 30e0a4db46..be6b1e0845 100644
--- a/tutorial/practicals/LFRic/building_code/2_built_ins/README.md
+++ b/tutorial/practicals/LFRic/building_code/2_built_ins/README.md
@@ -202,7 +202,7 @@ below).
 As each `invoke` call generates a PSy-layer subroutine (see the
 *Step 3* below for the algorithm code processing), it can be
 easier to specify a [label (name) for an `invoke`](
-https://psyclone.readthedocs.io/en/stable/introduction_to_psykal.html#algorithm-layer)
+https://psyclone.readthedocs.io/en/latest/user_guide/introduction_to_psykal.html#algorithm-layer)
 (and hence the subroutine) call to make it easier to search for in the
 generated code. To do this here modify the completed `invoke` by adding a
 name in the first line of the `invoke` call, e.g.
diff --git a/tutorial/practicals/LFRic/building_code/4_psydata/README.md b/tutorial/practicals/LFRic/building_code/4_psydata/README.md
index 7a8843b969..91d62065b8 100755
--- a/tutorial/practicals/LFRic/building_code/4_psydata/README.md
+++ b/tutorial/practicals/LFRic/building_code/4_psydata/README.md
@@ -213,7 +213,7 @@ perturbation_data .0000000E+00 .0000000E+00 .0000000E+00 .1000000E+01 .1000000E+
 The driver read in the data of the kernel data file, executed the driver, and compared the results
 with the results collected during the original execution. The table above is a summary of the
 comparison of all output variables. The meaning of these fields are explained in the
-[driver summary staticstics](https://psyclone.readthedocs.io/en/stable/psyke.html#driver-summary-statistics)
+[driver summary staticstics](https://psyclone.readthedocs.io/en/latest/user_guide/psyke.html#driver-summary-statistics)
 section of the manual.
 
 ## Step 8: Try other PSyData libraries
@@ -296,7 +296,7 @@ and ``Makefile.value_range_check`` for the makefile to use.
 
 This example by itself will not print any message (since there is no invalid floating
 point number). In order to define a range for a variable (see
-[the documentation](https://psyclone.readthedocs.io/en/stable/psy_data.html#value-range-check)
+[the documentation](https://psyclone.readthedocs.io/en/latest/user_guide/psy_data.html#value-range-check)
 for details), set the following environment variable:
 
     PSYVERIFY__time_evolution__perturbation_data=0:4000 ./time_evolution
diff --git a/tutorial/practicals/LFRic/building_code/README.md b/tutorial/practicals/LFRic/building_code/README.md
index a44158b79c..e5644a90da 100644
--- a/tutorial/practicals/LFRic/building_code/README.md
+++ b/tutorial/practicals/LFRic/building_code/README.md
@@ -132,7 +132,7 @@ in all tutorials. See, for instance, this code from the
 ```
 
 and [here](
-https://psyclone.readthedocs.io/en/stable/psyclone_command.html) for more
+https://psyclone.readthedocs.io/en/latest/user_guide/psyclone_command.html) for more
 information on running the `psyclone` script.
 
 As in LFRic, the generated algorithm and PSy-layer source is not kept in
@@ -154,6 +154,6 @@ have the support for [distributed memory](../distributed_memory) (done
 via the [YAXT library](
 https://dkrz-sw.gitlab-pages.dkrz.de/yaxt) in LFRic). Also, none of
 the [PSyclone transformations](
-https://psyclone.readthedocs.io/en/stable/transformations.html) for
+https://psyclone.readthedocs.io/en/latest/user_guide/transformations.html) for
 the [shared memory](../single_node) support are applied here so the
 code is generated and run in serial.
diff --git a/tutorial/practicals/LFRic/distributed_memory/2_annexed_dofs/psyclone.cfg b/tutorial/practicals/LFRic/distributed_memory/2_annexed_dofs/psyclone.cfg
index 6d393dfc07..7f0eba4380 100644
--- a/tutorial/practicals/LFRic/distributed_memory/2_annexed_dofs/psyclone.cfg
+++ b/tutorial/practicals/LFRic/distributed_memory/2_annexed_dofs/psyclone.cfg
@@ -117,7 +117,7 @@ access_mapping = go_read: read, go_write: write, go_readwrite: readwrite
 # go_grid_{internal,whole}_{inner,outer}_{start,stop}
 # Details about the grid properties and their usage can be found in the
 # PSyclone documentation at:
-# https://psyclone.readthedocs.io/en/stable/gocean1p0.html#argument-metadata-meta-args
+# https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html#argument-metadata-meta-args
 grid-properties = go_grid_xstop: {0}%%grid%%subdomain%%internal%%xstop: scalar: integer,
                   go_grid_ystop: {0}%%grid%%subdomain%%internal%%ystop: scalar: integer,
                   go_grid_data: {0}%%data: array: real,
diff --git a/tutorial/practicals/LFRic/distributed_memory/3_overlapping_comms/psyclone.cfg b/tutorial/practicals/LFRic/distributed_memory/3_overlapping_comms/psyclone.cfg
index bec243211f..1ab56f568a 100644
--- a/tutorial/practicals/LFRic/distributed_memory/3_overlapping_comms/psyclone.cfg
+++ b/tutorial/practicals/LFRic/distributed_memory/3_overlapping_comms/psyclone.cfg
@@ -116,7 +116,7 @@ access_mapping = go_read: read, go_write: write, go_readwrite: readwrite
 # go_grid_{internal,whole}_{inner,outer}_{start,stop}
 # Details about the grid properties and their usage can be found in the
 # PSyclone documentation at:
-# https://psyclone.readthedocs.io/en/stable/gocean1p0.html#argument-metadata-meta-args
+# https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html#argument-metadata-meta-args
 grid-properties = go_grid_xstop: {0}%%grid%%subdomain%%internal%%xstop: scalar: integer,
                   go_grid_ystop: {0}%%grid%%subdomain%%internal%%ystop: scalar: integer,
                   go_grid_data: {0}%%data: array: real,
diff --git a/tutorial/practicals/LFRic/single_node/1_openmp/psyclone.cfg b/tutorial/practicals/LFRic/single_node/1_openmp/psyclone.cfg
index 6bff79e7bf..24fed9f700 100644
--- a/tutorial/practicals/LFRic/single_node/1_openmp/psyclone.cfg
+++ b/tutorial/practicals/LFRic/single_node/1_openmp/psyclone.cfg
@@ -116,7 +116,7 @@ access_mapping = go_read: read, go_write: write, go_readwrite: readwrite
 # go_grid_{internal,whole}_{inner,outer}_{start,stop}
 # Details about the grid properties and their usage can be found in the
 # PSyclone documentation at:
-# https://psyclone.readthedocs.io/en/stable/gocean1p0.html#argument-metadata-meta-args
+# https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html#argument-metadata-meta-args
 grid-properties = go_grid_xstop: {0}%%grid%%subdomain%%internal%%xstop: scalar: integer,
                   go_grid_ystop: {0}%%grid%%subdomain%%internal%%ystop: scalar: integer,
                   go_grid_data: {0}%%data: array: real,

From e4266a23b9250017a872c9cf2c07eb52c94c912a Mon Sep 17 00:00:00 2001
From: Sergi Siso <sergiesg@gmail.com>
Date: Mon, 21 Jul 2025 12:40:21 +0100
Subject: [PATCH 09/11] #3058 Test with linkcheck and fix internal relative
 links

---
 .github/linkspector.yml                                      | 3 ++-
 lib/README.md                                                | 5 -----
 .../LFRic/building_code/1_simple_kernels/part1/README.md     | 2 +-
 .../LFRic/building_code/1_simple_kernels/part2/README.md     | 2 +-
 .../LFRic/distributed_memory/1_distributed_memory/README.md  | 2 +-
 tutorial/practicals/generic/1_intro_psyir/README.md          | 2 +-
 6 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/.github/linkspector.yml b/.github/linkspector.yml
index 2b1c158d38..de6b613ebc 100644
--- a/.github/linkspector.yml
+++ b/.github/linkspector.yml
@@ -1,10 +1,11 @@
 dirs:
   - .
 useGitIgnore: true
+# This sometimes fail due to timeouts on slow responses, or unauthorised access
 ignorePatterns:
   - pattern: '^https://mybinder.org/v2/gh/stfc/psyclone'
   - pattern: '^https://codecov.io/gh/stfc/PSyclone'
-  - pattern: '^\.'
+  - pattern: '^https://code.metoffice.gov.uk/svn'
 replacementPatterns:
   - pattern: '^https:\/\/(psyclone.*\.readthedocs\.io\/en)\/stable$'
     replacement: 'https://$1/latest'
diff --git a/lib/README.md b/lib/README.md
index 31b8a71d0b..36fcf1296f 100644
--- a/lib/README.md
+++ b/lib/README.md
@@ -51,11 +51,6 @@ rely on a file compiled in this directory.
 Contains code for extracting kernel data - i.e. all input and output
 parameters of a kernel invocation.
 
-### [``nan_test``](./nan_test) directory
-
-Contains PSyData-API-based libraries for checking that input and output
-parameters of kernels are valid numbers (i.e. not ``NaN`` or infinity).
-
 ### [``profiling``](./profiling) directory
 
 Contains PSyData-API-based wrapper libraries for various profiling libraries
diff --git a/tutorial/practicals/LFRic/building_code/1_simple_kernels/part1/README.md b/tutorial/practicals/LFRic/building_code/1_simple_kernels/part1/README.md
index 44296edaac..a1735becee 100644
--- a/tutorial/practicals/LFRic/building_code/1_simple_kernels/part1/README.md
+++ b/tutorial/practicals/LFRic/building_code/1_simple_kernels/part1/README.md
@@ -263,7 +263,7 @@ the LFRic repository).
 We will now run `make` to create the executable `simple_kernels_part1`
 using the provided [`simple_kernels_driver.f90`](simple_kernels_driver.f90)
 and the LFRic infrastructure [code support](
-../README.md#lfric-code-support). If the build is successful we can
+../../README.md#lfric-code-support). If the build is successful we can
 run the executable
 
 ```shell
diff --git a/tutorial/practicals/LFRic/building_code/1_simple_kernels/part2/README.md b/tutorial/practicals/LFRic/building_code/1_simple_kernels/part2/README.md
index a4c38fc59c..732075869e 100644
--- a/tutorial/practicals/LFRic/building_code/1_simple_kernels/part2/README.md
+++ b/tutorial/practicals/LFRic/building_code/1_simple_kernels/part2/README.md
@@ -249,7 +249,7 @@ The completed algorithm can be found in the
 We will now run `make` to create the executable `simple_kernels_part2`
 using the provided [`simple_kernels_driver.f90`](simple_kernels_driver.f90)
 and the LFRic infrastructure [code support](
-../README.md#lfric-code-support). If the build is successful we can
+../../README.md#lfric-code-support). If the build is successful we can
 run the executable
 
 ```shell
diff --git a/tutorial/practicals/LFRic/distributed_memory/1_distributed_memory/README.md b/tutorial/practicals/LFRic/distributed_memory/1_distributed_memory/README.md
index d51f06e20c..ecdfff1e7c 100644
--- a/tutorial/practicals/LFRic/distributed_memory/1_distributed_memory/README.md
+++ b/tutorial/practicals/LFRic/distributed_memory/1_distributed_memory/README.md
@@ -57,7 +57,7 @@ terminal.
 
 If the terminal output is not coloured you might like to install
 termcolor (`pip install termcolor` if using a virtualenv or take a
-look at the [installation instructions](../../../README.md#Requirements))
+look at the [installation instructions](../../../README.md##Requirements))
 and re-run.
 
 From inspection of the PSyIR you will see that the kernels are called
diff --git a/tutorial/practicals/generic/1_intro_psyir/README.md b/tutorial/practicals/generic/1_intro_psyir/README.md
index 8ec34eec36..7a3bf228c2 100644
--- a/tutorial/practicals/generic/1_intro_psyir/README.md
+++ b/tutorial/practicals/generic/1_intro_psyir/README.md
@@ -10,7 +10,7 @@ this mini-app was kindly provided by Silvia Mocavero of CMCC.
 ## Prerequisites ##
 
 The requirements for this section are as described in the practicals
-[README.md](../../README.md#Requirements).
+[README.md](../../README.md##Requirements).
 
 Check that PSyclone is installed and configured correctly by doing:
 

From 20280d393cc5895bf2818d33f4c1460519f37e69 Mon Sep 17 00:00:00 2001
From: Sergi Siso <sergiesg@gmail.com>
Date: Mon, 21 Jul 2025 12:43:21 +0100
Subject: [PATCH 10/11] #3058 Improve comment

---
 .github/linkspector.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/linkspector.yml b/.github/linkspector.yml
index de6b613ebc..2af501166b 100644
--- a/.github/linkspector.yml
+++ b/.github/linkspector.yml
@@ -1,7 +1,8 @@
 dirs:
   - .
 useGitIgnore: true
-# This sometimes fail due to timeouts on slow responses, or unauthorised access
+# Ignore URLs that sometimes fail due to timeouts on slow responses or
+# unauthorised accesses
 ignorePatterns:
   - pattern: '^https://mybinder.org/v2/gh/stfc/psyclone'
   - pattern: '^https://codecov.io/gh/stfc/PSyclone'

From 498ea36e755ae509198e30b64bd36aab10cd0490 Mon Sep 17 00:00:00 2001
From: Sergi Siso <sergiesg@gmail.com>
Date: Tue, 22 Jul 2025 15:15:31 +0100
Subject: [PATCH 11/11] #3058 Rename remaining instances of nan_test to
 value_range_check

---
 examples/lfric/scripts/KGOs/lfric_psyclone.cfg             | 2 +-
 examples/lfric/scripts/KGOs/lfric_psyclone_no_annexed.cfg  | 2 +-
 lib/README.md                                              | 7 ++++++-
 lib/value_range_check/lfric/README.md                      | 2 +-
 src/psyclone/tests/domain/nemo/test_files/nemo_test.cfg    | 2 +-
 .../LFRic/distributed_memory/2_annexed_dofs/psyclone.cfg   | 2 +-
 .../distributed_memory/3_overlapping_comms/psyclone.cfg    | 2 +-
 .../practicals/LFRic/single_node/1_openmp/psyclone.cfg     | 2 +-
 8 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/examples/lfric/scripts/KGOs/lfric_psyclone.cfg b/examples/lfric/scripts/KGOs/lfric_psyclone.cfg
index d1bf938f4c..809ce65efe 100644
--- a/examples/lfric/scripts/KGOs/lfric_psyclone.cfg
+++ b/examples/lfric/scripts/KGOs/lfric_psyclone.cfg
@@ -46,7 +46,7 @@ REPRODUCIBLE_REDUCTIONS = false
 # Amount to pad the local summation array when REPRODUCIBLE_REDUCTIONS is true
 REPROD_PAD_SIZE = 8
 PSYIR_ROOT_NAME = psyir_tmp
-VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, nan_test
+VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, value_range_check
 
 # Specify number of OpenCL devices per node. When combining OpenCL with MPI,
 # the mpirun/mpiexec ranks_per_node parameter must match this number.
diff --git a/examples/lfric/scripts/KGOs/lfric_psyclone_no_annexed.cfg b/examples/lfric/scripts/KGOs/lfric_psyclone_no_annexed.cfg
index d25dcef007..02731bd8bd 100644
--- a/examples/lfric/scripts/KGOs/lfric_psyclone_no_annexed.cfg
+++ b/examples/lfric/scripts/KGOs/lfric_psyclone_no_annexed.cfg
@@ -46,7 +46,7 @@ REPRODUCIBLE_REDUCTIONS = false
 # Amount to pad the local summation array when REPRODUCIBLE_REDUCTIONS is true
 REPROD_PAD_SIZE = 8
 PSYIR_ROOT_NAME = psyir_tmp
-VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, nan_test
+VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, value_range_check
 
 # Specify number of OpenCL devices per node. When combining OpenCL with MPI,
 # the mpirun/mpiexec ranks_per_node parameter must match this number.
diff --git a/lib/README.md b/lib/README.md
index 36fcf1296f..2e91dd4c0a 100644
--- a/lib/README.md
+++ b/lib/README.md
@@ -51,6 +51,11 @@ rely on a file compiled in this directory.
 Contains code for extracting kernel data - i.e. all input and output
 parameters of a kernel invocation.
 
+### [``value_range_check``](./value_range_check) directory
+
+Contains PSyData-API-based libraries for checking that input and output
+values of kernels are within valid ranges (i.e. not ``NaN`` or infinity).
+
 ### [``profiling``](./profiling) directory
 
 Contains PSyData-API-based wrapper libraries for various profiling libraries
@@ -107,7 +112,7 @@ is by default set to the relative path to the top-level `lib` directory.
 libraries are compiled in a clone of PSyclone repository or in a PSyclone
 [installation](#installation).
 
-Compilation of ``extract``, ``nan_test``, ``read_only`` and some of the
+Compilation of ``extract``, ``values_ragne_check``, ``read_only`` and some of the
 profiling wrapper libraries depends on infrastructure libraries relevant
 to the API they are used for. [GOcean API](
 https://psyclone.readthedocs.io/en/latest/user_guide/gocean1p0.html) uses the
diff --git a/lib/value_range_check/lfric/README.md b/lib/value_range_check/lfric/README.md
index 2263a950d3..f326e95065 100644
--- a/lib/value_range_check/lfric/README.md
+++ b/lib/value_range_check/lfric/README.md
@@ -77,7 +77,7 @@ The application needs to provide the parameters to link in this
 ``lfric``. For instance:
 
 ```shell
-$(F90)  ... -L$(PSYDATA_LIB_DIR)/nan_test/lfric -l_value_range_check \
+$(F90)  ... -L$(PSYDATA_LIB_DIR)/value_range_check/lfric -l_value_range_check \
         -L$(LFRIC_INF_DIR) -llfric $(LFRIC_SPECIFIC_LINKING_PARAMETERS)
 ```
 
diff --git a/src/psyclone/tests/domain/nemo/test_files/nemo_test.cfg b/src/psyclone/tests/domain/nemo/test_files/nemo_test.cfg
index 3b265cb6ba..b4df0e0913 100644
--- a/src/psyclone/tests/domain/nemo/test_files/nemo_test.cfg
+++ b/src/psyclone/tests/domain/nemo/test_files/nemo_test.cfg
@@ -47,7 +47,7 @@ REPRODUCIBLE_REDUCTIONS = false
 # Amount to pad the local summation array when REPRODUCIBLE_REDUCTIONS is true
 REPROD_PAD_SIZE = 8
 PSYIR_ROOT_NAME = psyir_tmp
-VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, nan_test
+VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, value_range_check
 
 # Specify number of OpenCL devices per node. When combining OpenCL with MPI,
 # the mpirun/mpiexec ranks_per_node parameter must match this number.
diff --git a/tutorial/practicals/LFRic/distributed_memory/2_annexed_dofs/psyclone.cfg b/tutorial/practicals/LFRic/distributed_memory/2_annexed_dofs/psyclone.cfg
index 7f0eba4380..d00f68c39f 100644
--- a/tutorial/practicals/LFRic/distributed_memory/2_annexed_dofs/psyclone.cfg
+++ b/tutorial/practicals/LFRic/distributed_memory/2_annexed_dofs/psyclone.cfg
@@ -47,7 +47,7 @@ REPRODUCIBLE_REDUCTIONS = false
 # Amount to pad the local summation array when REPRODUCIBLE_REDUCTIONS is true
 REPROD_PAD_SIZE = 8
 PSYIR_ROOT_NAME = psyir_tmp
-VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, nan_test
+VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, value_range_check
 
 # Specify number of OpenCL devices per node. When combining OpenCL with MPI,
 # the mpirun/mpiexec ranks_per_node parameter must match this number.
diff --git a/tutorial/practicals/LFRic/distributed_memory/3_overlapping_comms/psyclone.cfg b/tutorial/practicals/LFRic/distributed_memory/3_overlapping_comms/psyclone.cfg
index 1ab56f568a..5a26709b01 100644
--- a/tutorial/practicals/LFRic/distributed_memory/3_overlapping_comms/psyclone.cfg
+++ b/tutorial/practicals/LFRic/distributed_memory/3_overlapping_comms/psyclone.cfg
@@ -46,7 +46,7 @@ REPRODUCIBLE_REDUCTIONS = false
 # Amount to pad the local summation array when REPRODUCIBLE_REDUCTIONS is true
 REPROD_PAD_SIZE = 8
 PSYIR_ROOT_NAME = psyir_tmp
-VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, nan_test
+VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, value_range_check
 
 # Specify number of OpenCL devices per node. When combining OpenCL with MPI,
 # the mpirun/mpiexec ranks_per_node parameter must match this number.
diff --git a/tutorial/practicals/LFRic/single_node/1_openmp/psyclone.cfg b/tutorial/practicals/LFRic/single_node/1_openmp/psyclone.cfg
index 24fed9f700..2b905352fc 100644
--- a/tutorial/practicals/LFRic/single_node/1_openmp/psyclone.cfg
+++ b/tutorial/practicals/LFRic/single_node/1_openmp/psyclone.cfg
@@ -46,7 +46,7 @@ REPRODUCIBLE_REDUCTIONS = false
 # Amount to pad the local summation array when REPRODUCIBLE_REDUCTIONS is true
 REPROD_PAD_SIZE = 8
 PSYIR_ROOT_NAME = psyir_tmp
-VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, nan_test
+VALID_PSY_DATA_PREFIXES = profile, extract, read_only_verify, value_range_check
 
 # Specify number of OpenCL devices per node. When combining OpenCL with MPI,
 # the mpirun/mpiexec ranks_per_node parameter must match this number.