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Lintian error

I am getting this error from lintian

N:   This package contains an embedded copy of the JQuery, Prototype,
N:   Mochikit or "Cropper" JavaScript libraries that are now available in
N:   their own packages. Please depend on the appropriate package and
N:   symlink the library into the appropriate location.
N: N: Refer to Policy Manual, section 4.13 for details.

I have contacted upstream about this error, and he states that he would not want to depend on the prototype package in debian because he has made changes to the version of prototype he is currently using. I have run a diff on prototype which is in the package and the version in debian and there are differences.
Would Debian Policy 4.13 still apply?


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