Try listing the tar archive with the hardlink. For example:

$ tar -tvf test.tar
drwxr-xr-x 0/0       0 2016-07-13 00:00 t/
drwxr-xr-x 0/0       0 2016-07-13 00:00 t/foo/
-rw-r--r-- 0/0       7 2016-07-13 00:00 t/foo/A
drwxr-xr-x 0/0       0 2016-07-13 00:00 t/bar/
hrw-r--r-- 0/0       0 2016-07-13 00:00 t/bar/B link to t/foo/A

The equivalent of ln t/foo/A t/bar/B is performed when extracting such an archive. However, you have chosen to flatten the directory structure and extract all files in one target directory. In this case, linking will fail because the source file cannot be found in its expected location. (The t/foo/A is now outdir/A instead.)

I would suggest performing the operation in two stages: first to extract the files as usual, then flattening the directory.

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