Improve linearfold/linearpartition patchfiles to not include whitespace differences

[luxaritas]

Right now in README_LinearFold-E_patch.md, we specify that git apply should be called with --whitespace=fix. This is presumably necessary because there is some mismatch between the whitespace present in a fresh clone and the whitespace detected when creating the patch. To simplify patch file application (and improve compatibility with patch(1)), it would be best if we could re-generate these patchfiles without the conflicting whitespace