This is what I needed for my dockerfile to make this work.
FROM alpine:latest AS builder
WORKDIR /
RUN apk add build-base git automake autoconf libtool m4
RUN git clone https://github.com/netdata/libjudy
RUN mkdir -p /libjudy/doc/man/man3
RUN cd /libjudy && sed -i 's/automake-1.9/automake/' bootstrap && ./bootstrap && ./configure && make install
The man3 directory is a makefile oversight but I have no idea how to correctly fix it. The sed automake hack seems to work for now, but might break in the future. There are some warnings about old names being used in configure.ac.