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

10 files changed, 120 insertions, 0 deletions

diff --git a/tools/test/h5diff/testfiles/h5diff_10.txt b/tools/test/h5diff/testfiles/h5diff_10.txt
index b5ff01a..3631db7 100644
--- a/tools/test/h5diff/testfiles/h5diff_10.txt
+++ b/tools/test/h5diff/testfiles/h5diff_10.txt
@@ -143,6 +143,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_600.txt b/tools/test/h5diff/testfiles/h5diff_600.txt
index f52d8cc..8a4ce6d 100644
--- a/tools/test/h5diff/testfiles/h5diff_600.txt
+++ b/tools/test/h5diff/testfiles/h5diff_600.txt
@@ -143,6 +143,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_603.txt b/tools/test/h5diff/testfiles/h5diff_603.txt
index 84111b3..d4c7336 100644
--- a/tools/test/h5diff/testfiles/h5diff_603.txt
+++ b/tools/test/h5diff/testfiles/h5diff_603.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_606.txt b/tools/test/h5diff/testfiles/h5diff_606.txt
index d915d36..3123587 100644
--- a/tools/test/h5diff/testfiles/h5diff_606.txt
+++ b/tools/test/h5diff/testfiles/h5diff_606.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_612.txt b/tools/test/h5diff/testfiles/h5diff_612.txt
index 1ef8cdf..ce2d887 100644
--- a/tools/test/h5diff/testfiles/h5diff_612.txt
+++ b/tools/test/h5diff/testfiles/h5diff_612.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_615.txt b/tools/test/h5diff/testfiles/h5diff_615.txt
index 881362e..61fd036 100644
--- a/tools/test/h5diff/testfiles/h5diff_615.txt
+++ b/tools/test/h5diff/testfiles/h5diff_615.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_621.txt b/tools/test/h5diff/testfiles/h5diff_621.txt
index ba39a99..dc8655d 100644
--- a/tools/test/h5diff/testfiles/h5diff_621.txt
+++ b/tools/test/h5diff/testfiles/h5diff_621.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_622.txt b/tools/test/h5diff/testfiles/h5diff_622.txt
index 70421fc..f20ffbe 100644
--- a/tools/test/h5diff/testfiles/h5diff_622.txt
+++ b/tools/test/h5diff/testfiles/h5diff_622.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_623.txt b/tools/test/h5diff/testfiles/h5diff_623.txt
index 0d74268..f73d202 100644
--- a/tools/test/h5diff/testfiles/h5diff_623.txt
+++ b/tools/test/h5diff/testfiles/h5diff_623.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error
 
diff --git a/tools/test/h5diff/testfiles/h5diff_624.txt b/tools/test/h5diff/testfiles/h5diff_624.txt
index cb8b8b4..903b738 100644
--- a/tools/test/h5diff/testfiles/h5diff_624.txt
+++ b/tools/test/h5diff/testfiles/h5diff_624.txt
@@ -144,6 +144,18 @@ usage: h5diff [OPTIONS] file1 file2 [obj1[ obj2]]
       (The option --follow-symlinks overrides the default behavior when
        symbolic links are compared.).
 
+ Subsetting options:
+  Subsetting is available by using the fcompact form of subsetting, as follows:
+    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]
+  It is not required to use all parameters, but until the last parameter value used,
+  all of the semicolons (;) are required, even when a parameter value is not specified. Example:
+    obj1 /foo/mydataset[START;;COUNT;BLOCK]
+    obj1 /foo/mydataset[START]
+  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in
+  each dimension. START is optional and will default to 0 in each dimension.
+  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with
+  one integer for each dimension of the dataset.
+
  Exit code:
   0 if no differences, 1 if differences found, 2 if error