This is an interesting idea, but it doesn't seem easy to implement properly. Quilt isn't only about calling "patch" to apply patches. It is also relying on "diff" to display the changes and to refresh patches. In the case of coccinelle, refreshing doesn't make sense. "quilt diff" should probably display the patch generated by coccinelle rather than the semantic patch.

More generally, quilt needs to know the patch format to be able to find out which files are modified by a patch, in order to backup and restore them on push and pop, respectively. But as I understand it, coccinelle patches do not include file names, as they describe generic transformations.

So you would also need a way to add the target file information, either as formatted comments in the coccinelle patch files, or maybe as extra parameters in the series file. As the user, how would you like to provide this information? In any case, this would require checking and modifying a lot of code paths in quilt.

So I don't think this generic feature request can be implemented. Specifically adding support for coccinelle may be possible, but only after defining more clearly the expectations on each quilt command for such a patch format.