As I see it, the `Makefile.am` changes are backward-compatible. Thus I am not 
sure where the problem lies?

A few comments:
 - You should not bundle (other projects) m4 files in Git; these files are 
considered as development files and should be included in the relevant 
`-dev(el)` packages in your favorite distro.
 - If you really *must* trick `aclocal`, you can increase the `#serial` line so 
that it always picks the one in the repo. But you should not.
 - Do you really want Python 2 support? If not, I think Python 3 is distributed 
with a `pkg-config` file which you should definitely use. Maybe add a 
`./configure --with-python={2|3}` switch?

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