Lots of stuff here, hope it's useful! You write:

        'PDL::Core'       => '2.028',
[download]

but you should currently aim to depend on PDL not PDL::Core, at the version appropriate for your application. The version of PDL::Core is currently not updated on each release, only that of the PDL package itself, to ease the release process. This would look like (if your application needed a feature in the most recent release of PDL at the time of this writing):

        'PDL' => '2.080',
[download]

Also, your distro metadata points at EUMM's repo, which I am 100% sure is not what you intend:

                url  =>
                  'git://github.com/Perl-Toolchain-Gang/ExtUtils-MakeM
+aker.git',
                web =>
                  'https://github.com/Perl-Toolchain-Gang/ExtUtils-Mak
+eMaker',
[download]

Other nits are that your GitHub repo has your Makefile, Makefile.old, various META files, which I am also 100% sure is not what you intend. I also doubt that your README_TO_INSTALL is very useful, and might be more so if it just recommended using a CPAN client, then running the application.

Finally, it looks like your lib/App/README.md would be far more useful at the top level :-)