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Convert build process to use autotools (autoconf, automake, etc.)
This commit converts the build process from a hand-written Makefile that works on Linux, FreeBSD, and macOS, to an automatically generated Makefile managed by the autotools toolset. This incldues: * Add the compile, config.guess, config.sub, depcomp, install-sh, and missing helper scripts that autotools requires to be shipped with the package in order for configure to work. * Rename Makefile to Makefile.am and restructure it for compatibility with autotools and specifically with the stuff in our configure script. * Create the configure.ac source file which is turned into the configure script. * Rename Doxyfile to Doxyfile.in so that the source directories can be substituted into it at configure time. * Tweak .gitignore to ignore temporary and output files related to autotools. * Generate Makefile.in, aclocal.m4, and configure using `autoreconf` and include them as checked-in source files. While I can't fully document how autotools works here the basic workflow is that when you need to make changes to the build, you update Makefile.am and/or configure.ac as needed, run `autoreconf`, and commit the changes you made as well as any resulting changes to Makefile.in, aclocal.m4, and configure. Makefile should _not_ be committed into the source tree; it should always be generated using configure on the system where the build is being run.
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