[Doc] Resolve some links to the new doc structure

Also remove some obsolete "work in progress" admonitions.

doc/doxygen/mainpage.md

@@ -1,10 +1,7 @@
 # %Cantera C++ Reference
 
-> **Note:** This is the **%Cantera Developer API** documentation; for general
-> information on %Cantera, refer to [**cantera.org**](https://cantera.org).
-
-Use sidebar or menu at the top to view detailed documentation of the code, or
-use the following shortcuts:
+Use sidebar to view detailed documentation of the C++ code, or use the following
+shortcuts:
 
 * Overview of [**Cantera C++ Modules**](modules.html)
 * Index of [**Cantera C++ Classes**](classes.html)
@@ -20,7 +17,7 @@ A topical overview is provided as follows:
 * @ref physConstants (universal constants, built into %Cantera for convenience)
 
 For fundamental scientific theory used for the implementation of %Cantera, refer to the
-[Cantera Science Section](https://cantera.org/science/index.html) of the
-[Cantera Website](https://cantera.org).
+[Cantera Science Section](../reference/index.html#science-reference)
+of the [Cantera Website](https://cantera.org).
 
 The %Cantera source code is hosted on [GitHub](https://github.com/Cantera/cantera).

doc/sphinx/develop/index.md

@@ -1,10 +1,5 @@
 # Develop
 
-```{caution}
-This page is a work in progress. For compilation instructions for Cantera 3.0, please
-see <a href="/install/compiling-install.html">this page</a>.
-```
-
 (sec-compiling)=
 ## Compiling Cantera from Source
 
@@ -36,6 +31,10 @@ compiling/special-cases
 
 ## How Cantera Works
 
+```{caution}
+This section is a work in progress.
+```
+
 - [](reactor-integration)
 
 ```{toctree}
@@ -47,3 +46,7 @@ reactor-integration
 ```
 
 ## Adding New Models to Cantera
+
+```{caution}
+This section is a work in progress.
+```

doc/sphinx/python/ck_conversion.rst

@@ -3,9 +3,9 @@ Chemkin to YAML conversion
 **************************
 
 .. seealso::
-    For documentation of the command line interface, see the :ref:`ck2yaml
-    <sec-ck2yaml>` section. For a tutorial, refer to the `Converting Chemkin-format
-    files <https://cantera.org/tutorials/ck2yaml-tutorial.html>`_ pages.
+    For documentation of the command line interface, see the
+    :ref:`ck2yaml <sec-ck2yaml>` section. For a tutorial, refer to the
+    :doc:`/userguide/ck2yaml-tutorial` page.
 
 Module-level documentation
 ==========================

doc/sphinx/python/cti_conversion.rst

@@ -3,9 +3,9 @@ CTI to YAML conversion
 ***********************
 
 .. seealso::
-    For documentation of the command line interface, see the :ref:`cti2yaml
-    <sec-cti2yaml>` section. For a tutorial, refer to the `Converting CTI and XML input
-    files to YAML <https://cantera.org/tutorials/legacy2yaml.html>`_ pages.
+    For documentation of the command line interface, see the
+    :ref:`cti2yaml <sec-cti2yaml>` section. For a tutorial, refer to the
+    :doc:`/userguide/legacy2yaml-tutorial` page.
 
 Module-level documentation
 ==========================

doc/sphinx/python/ctml_conversion.rst

@@ -3,9 +3,9 @@ CTML to YAML conversion
 ***********************
 
 .. seealso::
-   For documentation of the command line interface, see the :ref:`ctml2yaml
-   <sec-ctml2yaml>` section. For a tutorial, refer to the `Converting CTI and XML input
-   files to YAML <https://cantera.org/tutorials/legacy2yaml.html>`_ pages.
+   For documentation of the command line interface, see the
+   :ref:`ctml2yaml <sec-ctml2yaml>` section. For a tutorial, refer to the
+   :doc:`/userguide/legacy2yaml-tutorial` page.
 
 
 Module-level documentation

doc/sphinx/reference/index.md

@@ -3,13 +3,6 @@
 
 This pages provide detailed reference documentation for Cantera.
 
-```{caution}
-This page is a work in progress. For more complete documentation of the current Cantera
-release (Cantera 3.0), please see the
-<a href="/documentation/index.html">documentation index</a> and the
-<a href="science/index.html">Science & Theory Manual</a>.
-```
-
 ## Programming Reference
 
 These sections document the classes and functions that define the Cantera interface for

doc/sphinx/reference/reactors/index.md

@@ -3,11 +3,6 @@
 
 # Reactors and Reactor Networks
 
-```{caution}
-This page is a work in progress. For more complete documentation of the current Cantera
-release (Cantera 3.0), please see <a href="/science/reactors/reactors.html">this page</a>.
-```
-
 In Cantera, a *reactor network* represents a set of one or more homogeneous reactors and
 reacting surfaces that may be connected to each other and to the environment through
 devices representing mass flow, heat transfer, and moving walls. The system is generally

doc/sphinx/userguide/ck2yaml-tutorial.md

@@ -195,10 +195,9 @@ Column 79 is blank; and finally, the row is ended in column 80 with the integer
 
 #### Lines 2--4
 
-% TODO: Link to NASA polynomials section in Science docs
-
 The next three lines of the thermodynamic entry have a similar format. They contain the
-coefficients of the 7-coefficient polynomial formulation in two temperature regions.
+coefficients of the [7-coefficient polynomial formulation](sec-thermo-nasa7) in two
+temperature regions.
 
 The second row of the thermo entry (the first after the information row) contains the
 first five coefficients that apply to the temperature range between the midpoint and the

doc/sphinx/userguide/index.md

@@ -1,10 +1,5 @@
 # User Guide
 
-```{caution}
-This page is a work in progress. For tutorials covering the current Cantera
-release (Cantera 3.0), please see <a href="/tutorials/index.html">this page</a>.
-```
-
 ## Introductory Tutorials
 
 For those new to Cantera, we present here a set of short tutorials to familiarize you

doc/sphinx/userguide/python-tutorial.md

@@ -199,9 +199,8 @@ Cantera search path:
 ct.add_directory('~/cantera/my_data_files')
 ```
 
-% TODO: Add link to input file guide
 Cantera input files are plain text files, and can be created with any text editor. See
-the document `Working With Input Files` for more information.
+the page [](input-tutorial) for more information.
 
 A Cantera input file may contain more than one phase specification, or may contain
 specifications of interfaces (surfaces). Here we import definitions of two bulk phases
@@ -220,9 +219,8 @@ passed as arguments to {py:class}`Interface`.
 
 ## Converting CK-format files
 
-% TODO: Add link to the ck2yaml guide
-`Converting CK-format Files` documentation for information on how to convert from
-CK-format to Cantera's YAML format.
+See the page [](ck2yaml-tutorial) for information on how to convert from CK-format to
+Cantera's YAML format.
 
 ## Getting Help
 

doc/sphinx/userguide/thermobuild.md

@@ -1,11 +1,11 @@
 (sec-thermobuild)=
 # Converting Data from NASA ThermoBuild
 
-% TODO: Link to NASA9 Science docs
-
 Thermodynamic data for a range of species can be obtained from the
 [NASA ThermoBuild](https://cearun.grc.nasa.gov/ThermoBuild/index_ds.html) tool.
-This thermodynamic data is described using the 9-coefficient NASA polynomial parameterization, which is implemented by Cantera.
+This thermodynamic data is described using the
+[9-coefficient NASA polynomial](sec-thermo-nasa9) parameterization, which is implemented
+by Cantera.
 
 To generate an input file containing thermodynamic data, use the ThermoBuild web
 interface to select the elements you want to include, and click *process*. Then, select

doc/sphinx/yaml/ck2yaml.rst

@@ -5,8 +5,7 @@ Chemkin to YAML conversion
 **************************
 
 .. seealso::
-    For a tutorial, refer to the `Converting Chemkin-format files
-    <https://cantera.org/tutorials/ck2yaml-tutorial.html>`_ pages.
+    For a tutorial, refer to the :doc:`/userguide/ck2yaml-tutorial` page.
 
 .. argparse::
    :module: cantera.ck2yaml