Documentation updates

docs/src/site/_data/sidebars/netcdfJavaTutorial_sidebar.yml

@@ -150,135 +150,146 @@ entries:
   - title: netCDF-Java Reference Docs
     output: web, pdf
     folderitems:
-
-    - title: ArrayStructures
-      url: /arraystructures_ref.html
-      output: web, pdf
-
-    - title: BUFR Files
-      url: /bufr_processing.html
-      output: web, pdf
-
-    - title: BUFR Tables
-      url: /bufr_tables.html
-      output: web, pdf
-
-    - title: CDM File Types
-      url: /file_types.html
-      output: web, pdf
-
-    - title: CDM Calendar Date Handling
-      url: /cdm_calendar_date_time_ref.html
-      output: web, pdf
-
-    - title: CDM Disk Caching
-      url: /disk_caching.html
-      output: web, pdf
-
-    - title: CDMRemote
-      url: /cdmremote.html
-      output: web, pdf
-
-    - title: CDMRemote Feature Datasets
-      url: /cdmremote_feature_datasets.html
-      output: web, pdf
-
-    - title: CDM to NetCDF Mapping
-      url: /cdm_netcdf_mapping.html
-      output: web, pdf
-
-    - title: CDM - OPeNDAP Interface
-      url: /cdm_opendap_interface.html
-      output: web, pdf
-
-    - title: NetCDF4 Compound Attributes
-      url: /cdm_netcdf_mapping.html
-      output: web, pdf
+    - output: web, pdf
+      subfolders:
+        - title: More API
+          output: web, pdf
+          subfolderitems:
+            - title: ArrayStructures
+              url: /arraystructures_ref.html
+              output: web, pdf
+
+            - title: CDM Calendar Date Handling
+              url: /cdm_calendar_date_time_ref.html
+              output: web, pdf
+
+            - title: CDM Disk Caching
+              url: /disk_caching.html
+              output: web, pdf
+            - title: Dataset URLs
+              url: /dataset_urls.html
+              output: web, pdf
+
+            - title:  Forecast Model Run Collection
+              url: /fmrc_ref.html
+              output: web, pdf
+
+            - title: netCDF C Library
+              url: /netcdf4_c_library.html
+              output: web, pdf
+
+            - title: PointFeature Reference
+              url: /pointfeature_ref.html
+              output: web, pdf
+
+            - title: Standard Horizontal Coordinate Transforms
+              url: /std_horizonal_coord_transforms.html
+              output: web, pdf
+
+            - title: Unidata Defined System Properties
+              url: /systemproperties.html
+              output: web, pdf
+        - title: Common Data Model Mappings
+          output: web, pdf
+          subfolderitems:
+          - title: CDM to NetCDF Mapping
+            url: /cdm_netcdf_mapping.html
+            output: web, pdf
+
+          - title: CDM - OPeNDAP Interface
+            url: /cdm_opendap_interface.html
+            output: web, pdf
+        - title: Conventions
+          output: web, pdf
+          subfolderitems:
+          - title: CF DSG Encoding Table
+            url: /cf_dsg_encoding_ref.html
+            output: web, pdf
+
+          - title: Coordinate Attribute Convention
+            url: /coord_attr_conv.html
+            output: web, pdf
+
+        - title: Data Formats
+          output: web, pdf
+          subfolderitems:
+          - title: CDM File Types
+            url: /file_types.html
+            output: web, pdf
+
+          - title: BUFR Files
+            url: /bufr_processing.html
+            output: web, pdf
+
+          - title: BUFR Tables
+            url: /bufr_tables.html
+            output: web, pdf
+          - title: GRIB Files in CDM
+            url: /grib_files_cdm.html
+            output: web, pdf
+
+          - title: GRIB Tables in CDM
+            url: /grib_tables.html
+            output: web, pdf
+
+          - title: GRIB Collection Specification
+            url: /grib_feature_collections_ref.html
+            output: web, pdf
+
+          - title: Reading Zarr
+            url: /reading_zarr.html
+            output: web, pdf
+
+        - title: Remote Access
+          output: web, pdf
+          subfolderitems:
+          - title: Read CDM files over HTTP
+            url: /read_over_http.html
+            output: web, pdf
+
+          - title: CDMRemote
+            url: /cdmremote.html
+            output: web, pdf
+
+          - title: CDMRemote Feature Datasets
+            url: /cdmremote_feature_datasets.html
+            output: web, pdf
+
+          - title: NC Stream
+            url: /ncstream.html
+            output: web, pdf
+
+          - title: NC Stream Grammar
+            url: /ncstream_grammar.html
+            output: web, pdf
+
+          - title: NetCDF Subset Service
+            external_url: https://docs.unidata.ucar.edu/tds/current/userguide/netcdf_subset_service_ref.html
+            output: web, pdf
+
+        - title: NcML
+          output: web, pdf
+          subfolderitems:
+          - title: NcML Overview
+            url: /ncml_overview.html
+            output: web, pdf
+
+          - title: NcML Cookbook
+            url: /ncml_cookbook.html
+            output: web, pdf
+
+          - title: Annotated Schema for NcML
+            url: /annotated_ncml_schema.html
+            output: web, pdf
 
     - title: CDM Utility Programs
       url: /cdm_utility_programs.html
       output: web, pdf
 
-    - title: CF DSG Encoding Table
-      url: /cf_dsg_encoding_ref.html
-      output: web, pdf
-
-    - title: Coordinate Attribute Convention
-      url: /coord_attr_conv.html
-      output: web, pdf
-
-    - title: Dataset URLs
-      url: /dataset_urls.html
-      output: web, pdf
-
-    - title:  Forecast Model Run Collection
-      url: /fmrc_ref.html
-      output: web, pdf
-
-    - title: GRIB Files in CDM
-      url: /grib_files_cdm.html
-      output: web, pdf
-
-    - title: GRIB Tables in CDM
-      url: /grib_tables.html
-      output: web, pdf
-
-    - title: GRIB Collection Specification
-      url: /grib_feature_collections_ref.html
-      output: web, pdf
-
-    - title: NcML Overview
-      url: /ncml_overview.html
-      output: web, pdf
-
-    - title: NcML Cookbook
-      url: /ncml_cookbook.html
-      output: web, pdf
-
-    - title: Annotated Schema for NcML
-      url: /annotated_ncml_schema.html
-      output: web, pdf
-
-    - title: NC Stream
-      url: /ncstream.html
-      output: web, pdf
-
-    - title: NC Stream Grammar
-      url: /ncstream_grammar.html
-      output: web, pdf
-
-    - title: netCDF-Java and TDS Doc Guide
-      url: /doc_guide.html
-      output: web, pdf
-
-    - title: NetCDF Subset Service
-      external_url: https://docs.unidata.ucar.edu/tds/current/userguide/netcdf_subset_service_ref.html
-      output: web, pdf
-
-    - title: netCDF C Library
-      url: /netcdf4_c_library.html
-      output: web, pdf
-
-    - title: PointFeature Reference
-      url: /pointfeature_ref.html
-      output: web, pdf
-
-    - title: Read CDM files over HTTP
-      url: /read_over_http.html
-      output: web, pdf
-
-    - title: Reading Zarr
-      url: /reading_zarr.html
-      output: web, pdf
-
-    - title: Standard Horizontal Coordinate Transforms
-      url: /std_horizonal_coord_transforms.html
-      output: web, pdf
-
     - title: ToolsUI Reference
       url: /toolsui_ref.html
       output: web, pdf
 
-    - title: Unidata Defined System Properties
-      url: /systemproperties.html
+    - title: netCDF-Java and TDS Doc Guide
+      url: /doc_guide.html
       output: web, pdf

docs/src/site/pages/netcdfJava/GribFilesCdm.md

@@ -151,7 +151,7 @@ You must generate the GRIB Collection index file in a [separate step](#creating-
 A GRIB file is an unordered collection of GRIB records.
 A GRIB record consists of a single 2D (x, y) slice of data.
 The CDM library reads a GRIB file and creates a 2, 3,4, or 5 dimension Variable (time, ensemble, z, y, x), by finding the records with the same parameter, with different time / level / ensemble coordinates.
-This amounts to [guessing the dataset schema](https://www.unidata.ucar.edu/blogs/developer/en/entry/dataset_schemas_are_lost_in){:target="_blank"} and the intent of the data provider, and is unfortunately a bit arbitrary. 
+This amounts to [guessing the dataset schema](https://www.unidata.ucar.edu/blogs/developer/entry/dataset_schemas_are_lost_in){:target="_blank"} and the intent of the data provider, and is unfortunately a bit arbitrary. 
 Most of our testing is against the NCEP operational models from the [IDD](https://www.unidata.ucar.edu/projects/index.html#idd){:target="_blank"}, and so are influenced by those.
 Deciding how to group the GRIB records into CDM Variables is one of the main source of problems.
 It uses the following GRIB fields to construct a unique variable.

docs/src/site/pages/netcdfJava/Upgrade.md

@@ -62,7 +62,7 @@ Please see the release notes on GitHub for more details on additions, enhancemen
 Point release notes:
 * [5.7.0](https://github.com/Unidata/netcdf-java/releases/tag/v5.7.0){:target="_blank"} (_2025-01-06_)
 
-5.7.x adds support for a service provider interface for applying enhancements by NSF Unidata summer intern Leo Matak (see https://www.unidata.ucar.edu/blogs/developer/en/entry/extensible-ncml-for-ai-ml for more information!).
+5.7.x adds support for a service provider interface for applying enhancements by NSF Unidata summer intern Leo Matak (see https://www.unidata.ucar.edu/blogs/developer/entry/extensible-ncml-for-ai-ml for more information!).
 BUFR support has been enhanced to include multi-category messages thanks to an external contribution from github user @Yaqiang!
 Please see the release notes on GitHub for more details on additions, enhancements, and bug fixes.
 
@@ -97,7 +97,7 @@ Point release notes:
 
 Much of the work in 5.4.x is focused on establishing a public API.
 We now publish two sets of javadocs - [with](../javadoc-with-deprecations/){:target="_blank"} and [without deprecations](../javadoc/){:target="_blank"}.
-For more information about these efforts and why this work is being done, please visit ([link](https://www.unidata.ucar.edu/blogs/developer/en/entry/netcdf-java-looking-ahead){:target="_blank"}).
+For more information about these efforts and why this work is being done, please visit ([link](https://www.unidata.ucar.edu/blogs/developer/entry/netcdf-java-looking-ahead){:target="_blank"}).
 Only those classes and methods outlined in the javadocs [without deprecations](../javadoc/) will exist in the next major release of netCDF-Java (`v6.0`).
 
 For more information about the changes in this release, please visit the [netCDF-Java github wiki](https://github.com/Unidata/netcdf-java/wiki#public-api-details){:target="_blank"}.

docs/src/site/pages/netcdfJava/faq.md

@@ -245,7 +245,7 @@ Netcdf-Java library supports writing netCDF-3 file format using the [classic dat
 
 #### Q: What is the relationship of NetCDF with HDF5?
 
-The netCDF-4 file format is built on top of the <a href="http://www.hdfgroup.org/HDF5/">HDF5 file format</a>. NetCDF adds shared dimensions, so it is unfortunately not a strict subset of HDF5. Gory details are here:  <a href="https://www.unidata.ucar.edu/blogs/developer/en/entry/dimensions_scales">Part 1</a>, <a href="https://www.unidata.ucar.edu/blogs/developer/en/entry/dimension_scale2">Part 2</a>, <a href="https://www.unidata.ucar.edu/blogs/developer/en/entry/dimension_scales_part_3">Part 3</a>.
+The netCDF-4 file format is built on top of the <a href="http://www.hdfgroup.org/HDF5/">HDF5 file format</a>. NetCDF adds shared dimensions, so it is unfortunately not a strict subset of HDF5. Gory details are here:  <a href="https://www.unidata.ucar.edu/blogs/developer/entry/dimensions_scales">Part 1</a>, <a href="https://www.unidata.ucar.edu/blogs/developer/entry/dimension_scale2">Part 2</a>, <a href="https://www.unidata.ucar.edu/blogs/developer/en/entry/dimension_scales_part_3">Part 3</a>.
 
 HDF5 is a very complicated format, and we do not plan to write a pure Java version for writing netCDF4 files (we do have a pure Java version for reading both HDF5 and netCDF-4). You must use the JNI interface to the [netCDF C library](netcdf4_c_library.html).
 

docs/src/site/pages/netcdfJava_tutorial/cdmdatasets/writing_netcdf.md

@@ -117,7 +117,7 @@ The following examples demonstrate several ways to write data to an opened file.
 #### Writing to a netCDF-4 file with compression (version 4.5)
 
 The main use of netCDF-4 is to get the performance benefits from compression, and possibly from chunking 
-([why it matters](https://www.unidata.ucar.edu/blogs/developer/en/entry/chunking_data_why_it_matters)). 
+([why it matters](https://www.unidata.ucar.edu/blogs/developer/entry/chunking_data_why_it_matters)). 
 By default, the Java library will use the default chunking algorithm to write chunked and compressed netcdf-4 files. 
 To control chunking and compression settings, you must create a `Nc4Chunking` object and pass it into `NetcdfFormatWriter.createNewNetcdf4`: