You are missing autoconf which is not installed with the command line tools. This is fine. Users are not expected to have the "autotools" in order to build an autotools project. This is the same as on Linux distress except that said tools are installed with the "build-essentials" while they are not on macOS.
These autogenerated scripts are not added to the git repo as they likely change all the time and should be generated instead without checking them in.
There are two ways to generate the configure script & makefiles (I recommend #1 for now):
1. I (or another developer/maintainer) create a distribution zip which has the configure script & makefiles already generated. This is equivalent to downloading source release. I've generated a distribution snapshot for you at
http://docs.danomatika.com/pdbuilds/. Download the pd-0.47.1-* zip, unpack, and run your build from it's directory. As a note, once an autotools project is configured, you can create a distribution zip using:
make dist
2. If you want to build from a clone from Github, you can install autoconf, automaker, & libtool, then the autopen script will work (this really only makes sense for developers). Easiest way to do this is to use
Homebrew. Once HB is installed:
brew install autoconf automake libtool