I was having trouble figuring out the correct patch command

Generally, patch -p0 < /tmp/the.patch suffices.

    diff -urd oldDir newDir > /tmp/the.patch

    head -n 1 /tmp/the.patch
    # directory should show as relative path,
    # e.g. oldDir/foo/bar/quux.pl

    cd oldDir/..
    # move above the directory to patch
    # to ensure we are in the correct position

    mv newDir newDir.disabled
    # it must not interfere with the
    # following test application of the patch

    patch -p0 < /tmp/the.patch

    mv newDir.disabled newDir
    # restore
[download]

submitting patches for whole distributions

Learn git, this will be the single most useful tool for contributing patches to Perl projects.

Is it normal, rather, to make a patch file for each changed file and submit all of them?

No, that's abnormal. Your usage of diff -urd was customary, i.e. make one patch each containing the all changes for one feature or bugfix across all files.

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