I've now checked also images from the 800D and 77D models:
DNG-Converter converts to 6024x4022, and DCRAW reports 6024x4020.

And I found that with both models the additional top rows of the DNGs are black!
So the correct size seems to be 6024x4020.
Since there is no chance to have a common and correct size, I think it might be the best to not change anything.

I'm afraid it's more basic than magic.

Typical today raw converter (e.g. Adobe's and/or in-camera JPEG generator, I'm not familiar with rawtherapee) applies S-shaped curve (with different parameters for different cameras/different ISO setting on same camera/different other setting e.g. DLO on Nikon cameras).
LibRaw/dcraw default rendering does histogram shift to the right only.

Here is your sample with +1 correction with highlights compression: https://www.dropbox.com/s/fsimdf5alou55qy/Screenshot%202019-01-25%2020.2...

The second one (_03.nef) is underexposed: https://www.dropbox.com/s/2jmz4niipiv552v/Screenshot%202019-01-25%2017.4...
(gray square on girl's cheek is RawDigger sample, average green/red is ~5EV below saturation point).

After exposure correction the image is more-or-less OK: https://www.dropbox.com/s/g76re8v887rnfen/Screenshot%202019-01-25%2017.4...

Checked the 1st one:

dcraw -w -T (and irfanview screenshot of resulting tiff file): https://www.dropbox.com/s/ynkb94latus6n55/Screenshot%202019-01-25%2017.0...

Embedded JPEG viewed via FastRawViewer: https://www.dropbox.com/s/wbc4ifjizd9dzm4/Screenshot%202019-01-25%2017.0...

This is screnshots from screen, so in (my) display colorspace (near-sRGB)

I do not see any big problems here, although LibRaw's color profile may differ from Nikon's one

Could you please provide some (properly exposed) samples with 'problematic' color/brightness?

Thanks.

Using your make procedure works!

But the document on this site says run ./configure, and since there is no configure file, I run mkdist.sh and it does create one.

Could you please update the build procedure?

Many thanks.

It just works as expected:

$ git clone https://github.com/LibRaw/LibRaw.git LibRaw-github
$ cd LibRaw-github
 
# edited simple_dcraw to get format printed:
$ git diff
diff --git a/samples/simple_dcraw.cpp b/samples/simple_dcraw.cpp
index 47c329a..78f14f0 100644
--- a/samples/simple_dcraw.cpp
+++ b/samples/simple_dcraw.cpp
@@ -145,7 +145,7 @@ int main(int ac, char *av[])
                  T.tformat == LIBRAW_THUMBNAIL_JPEG ? "thumb.jpg" : "thumb.ppm");
 
         if (verbose)
-          printf("Writing thumbnail file %s\n", thumbfn);
+          printf("Writing thumbnail file %s format: %d\n", thumbfn, T.tformat);
         if (LIBRAW_SUCCESS != (ret = RawProcessor.dcraw_thumb_writer(thumbfn)))
         {
           fprintf(stderr, "Cannot write %s: %s\n", thumbfn, libraw_strerror(ret));
 
# no autotools here, so just:
$ make -f Makefile.dist
 
# identify files:
$ ./bin/raw-identify ~/smpl/*
/Users/lexa/smpl/UNCOMPRESSED_14bit.ARW is a Sony ILCE-7M3 image.
/Users/lexa/smpl/_DSC0010.ARW is a Sony ILCE-7M3 image.
/Users/lexa/smpl/fuji_xh1_compressed.RAF is a Fujifilm X-H1 image.
/Users/lexa/smpl/fuji_xh1_uncompressed.RAF is a Fujifilm X-H1 image.
 
# run simple_dcraw -e -v:
$ ./bin/simple_dcraw -v -e ~/smpl/*
Processing file /Users/lexa/smpl/UNCOMPRESSED_14bit.ARW
Writing thumbnail file /Users/lexa/smpl/UNCOMPRESSED_14bit.ARW.thumb.jpg format: 1
Processing file /Users/lexa/smpl/_DSC0010.ARW
Writing thumbnail file /Users/lexa/smpl/_DSC0010.ARW.thumb.jpg format: 1
Processing file /Users/lexa/smpl/fuji_xh1_compressed.RAF
Writing thumbnail file /Users/lexa/smpl/fuji_xh1_compressed.RAF.thumb.jpg format: 1
Processing file /Users/lexa/smpl/fuji_xh1_uncompressed.RAF
Writing thumbnail file /Users/lexa/smpl/fuji_xh1_uncompressed.RAF.thumb.jpg format: 1

Could you please apply the patch shown above (print T.tformat in simple_dcraw -e) and check is tformat is really not 1.
Just change the line:
printf("Writing thumbnail file......
to
printf("Writing thumbnail file %s with format: %d\n", thumbfn,T.tformat);

Dear Sir:
We tried to reproduce the problem:
- fetched LibRaw/master from github to make sure
- compiled it with MSVC 2013.
- selected some sample files (Sony A7-3, Fuji X-H1):

raw-identify.exe fuji_xh1_compressed.RAF fuji_xh1_uncompressed.RAF _DSC0010.ARW UNCOMPRESSED_14bit.ARW:

fuji_xh1_compressed.RAF is a Fujifilm X-H1 image.
fuji_xh1_uncompressed.RAF is a Fujifilm X-H1 image.
_DSC0010.ARW is a Sony ILCE-7M3 image.
UNCOMPRESSED_14bit.ARW is a Sony ILCE-7M3 image.

Than I've modified simple_dcraw.cpp sample to print (numerical) format ID:

diff --git a/samples/simple_dcraw.cpp b/samples/simple_dcraw.cpp
index 47c329a..b079a9f 100644
--- a/samples/simple_dcraw.cpp
+++ b/samples/simple_dcraw.cpp
@@ -145,7 +145,7 @@ int main(int ac, char *av[])
T.tformat == LIBRAW_THUMBNAIL_JPEG ? "thumb.jpg" : "thumb.ppm");

if (verbose)
- printf("Writing thumbnail file %s\n", thumbfn);
+ printf("Writing thumbnail file %s with format: %d\n", thumbfn,T.tformat);
if (LIBRAW_SUCCESS != (ret = RawProcessor.dcraw_thumb_writer(thumbfn)))
{
fprintf(stderr, "Cannot write %s: %s\n", thumbfn, libraw_strerror(ret));

And here is the results:
simple_dcraw.exe -v -e _DSC0010.ARW fuji_xh1_compressed.RAF fuji_xh1_uncompressed.RAF UNCOMPRESSED_14bit.ARW:
Processing file _DSC0010.ARW
Writing thumbnail file _DSC0010.ARW.thumb.jpg with format: 1
Processing file fuji_xh1_compressed.RAF
Writing thumbnail file fuji_xh1_compressed.RAF.thumb.jpg with format: 1
Processing file fuji_xh1_uncompressed.RAF
Writing thumbnail file fuji_xh1_uncompressed.RAF.thumb.jpg with format: 1
Processing file UNCOMPRESSED_14bit.ARW
Writing thumbnail file UNCOMPRESSED_14bit.ARW.thumb.jpg with format: 1

From libraw_const.h:

enum LibRaw_thumbnail_formats
{
LIBRAW_THUMBNAIL_UNKNOWN = 0,
LIBRAW_THUMBNAIL_JPEG = 1,

So, all thumbnails format reported is LIBRAW_THUMBNAIL_JPEG

Please make sure you compile the library and your app with same libraw.h