Primary change is HDFFV-11212 - new refs and JNI (#372)

* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

7 files changed, 25 insertions, 25 deletions

diff --git a/java/examples/intro/H5_CreateAttribute.java b/java/examples/intro/H5_CreateAttribute.java
index 22b03ad..ab45039 100644
--- a/java/examples/intro/H5_CreateAttribute.java
+++ b/java/examples/intro/H5_CreateAttribute.java
@@ -28,10 +28,10 @@ public class H5_CreateAttribute {
     private static String DATASETATTRIBUTE = "Units";
 
     private static void CreateDatasetAttribute() {
-        long file_id = -1;
-        long dataspace_id = -1;
-        long dataset_id = -1;
-        long attribute_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataspace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long attribute_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims1 = { DIM_X, DIM_Y };
         long[] dims = { 2 };
         int[] attr_data = { 100, 200 };
diff --git a/java/examples/intro/H5_CreateDataset.java b/java/examples/intro/H5_CreateDataset.java
index 7b56e83..f376272 100644
--- a/java/examples/intro/H5_CreateDataset.java
+++ b/java/examples/intro/H5_CreateDataset.java
@@ -27,9 +27,9 @@ public class H5_CreateDataset {
     private static final int DIM_Y = 6;
 
     private static void CreateDataset() {
-        long file_id = -1;
-        long dataspace_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataspace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
 
         // Create a new file using default properties.
diff --git a/java/examples/intro/H5_CreateFile.java b/java/examples/intro/H5_CreateFile.java
index 367e61f..773df81 100644
--- a/java/examples/intro/H5_CreateFile.java
+++ b/java/examples/intro/H5_CreateFile.java
@@ -24,7 +24,7 @@ public class H5_CreateFile {
     static final String FILENAME = "H5_CreateFile.h5";
 
     private static void CreateFile() {
-        long file_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
 
         // Create a new file using default properties.
         try {
diff --git a/java/examples/intro/H5_CreateGroup.java b/java/examples/intro/H5_CreateGroup.java
index 54f6252..ab970e1 100644
--- a/java/examples/intro/H5_CreateGroup.java
+++ b/java/examples/intro/H5_CreateGroup.java
@@ -25,8 +25,8 @@ public class H5_CreateGroup {
     private static String GROUPNAME = "MyGroup";
 
     private static void CreateGroup() {
-        long file_id = -1;
-        long group_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long group_id = HDF5Constants.H5I_INVALID_HID;
 
         // Create a new file using default properties.
         try {
diff --git a/java/examples/intro/H5_CreateGroupAbsoluteRelative.java b/java/examples/intro/H5_CreateGroupAbsoluteRelative.java
index b9c35d7..ae142ae 100644
--- a/java/examples/intro/H5_CreateGroupAbsoluteRelative.java
+++ b/java/examples/intro/H5_CreateGroupAbsoluteRelative.java
@@ -27,10 +27,10 @@ public class H5_CreateGroupAbsoluteRelative {
     private static String GROUPNAME_B = "GroupB";
 
     private static void CreateGroupAbsoluteAndRelative() {
-        long file_id = -1;
-        long group1_id = -1;
-        long group2_id = -1;
-        long group3_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long group1_id = HDF5Constants.H5I_INVALID_HID;
+        long group2_id = HDF5Constants.H5I_INVALID_HID;
+        long group3_id = HDF5Constants.H5I_INVALID_HID;
 
         // Create a new file using default properties.
         try {
diff --git a/java/examples/intro/H5_CreateGroupDataset.java b/java/examples/intro/H5_CreateGroupDataset.java
index 191a21a..9657cf0 100644
--- a/java/examples/intro/H5_CreateGroupDataset.java
+++ b/java/examples/intro/H5_CreateGroupDataset.java
@@ -32,12 +32,12 @@ public class H5_CreateGroupDataset {
     private static final int DIM2_Y = 10;
 
     private static void h5_crtgrpd() {
-        long file_id = -1;
-        long dataspace_id = -1;
-        long dataset_id = -1;
-        long group_id = -1;
-        long group1_id = -1;
-        long group2_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataspace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long group_id = HDF5Constants.H5I_INVALID_HID;
+        long group1_id = HDF5Constants.H5I_INVALID_HID;
+        long group2_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset1_data = new int[DIM1_X][DIM1_Y];
         int[][] dset2_data = new int[DIM2_X][DIM2_Y];
         long[] dims1 = { DIM1_X, DIM1_Y };
@@ -108,7 +108,7 @@ public class H5_CreateGroupDataset {
         try {
             if (dataspace_id >= 0)
                 H5.H5Sclose(dataspace_id);
-            dataspace_id = -1;
+            dataspace_id = HDF5Constants.H5I_INVALID_HID;
         }
         catch (Exception e) {
             e.printStackTrace();
@@ -118,7 +118,7 @@ public class H5_CreateGroupDataset {
         try {
             if (dataset_id >= 0)
                 H5.H5Dclose(dataset_id);
-            dataset_id = -1;
+            dataset_id = HDF5Constants.H5I_INVALID_HID;
         }
         catch (Exception e) {
             e.printStackTrace();
diff --git a/java/examples/intro/H5_ReadWrite.java b/java/examples/intro/H5_ReadWrite.java
index 812ac77..82beec9 100644
--- a/java/examples/intro/H5_ReadWrite.java
+++ b/java/examples/intro/H5_ReadWrite.java
@@ -27,9 +27,9 @@ public class H5_ReadWrite {
     private static final int DIM_Y = 6;
 
     private static void ReadWriteDataset() {
-        long file_id = -1;
-        long dataspace_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataspace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];