Create a dir src and put the entire source tree in it.

Create configure.ac (or generate it with autoscan && mv configure.scan configure.ac and then hand-edit:

#                                               -*- Autoconf -*-                                                                                                                    
# Process this file with autoconf to produce a configure script.                                                                                                                    
                                                                                                                                                                    
AC_PREREQ([2.68])                                                                                                                                                                   
AC_INIT([mainfix], [0.00.00], [j.bokma@rug.nl])                                                                                                                                     
AM_INIT_AUTOMAKE([1.10 -Wall no-define foreign])                                                                                                                                    
AC_CONFIG_SRCDIR([src/main.cc])                                                                                                                                                     
AC_CONFIG_HEADERS([config.h])

# Checks for programs.
AC_PROG_CXX
AC_PROG_CC

# Checks for libraries.

# Checks for header files.

# Checks for typedefs, structures, and compiler characteristics.
AC_HEADER_STDBOOL
AC_C_INLINE
AC_TYPE_SIZE_T

# Checks for library functions.

AC_CONFIG_FILES([Makefile])
AC_OUTPUT
	  

Create Makefile.am by hand:

AUTOMAKE_OPTIONS = subdir-objects
ACLOCAL_AMFLAGS = ${ACLOCAL_FLAGS}

bin_PROGRAMS = mainfix
mainfix_SOURCES = src/main.cc \
src/angle/add.cc \
src/angle/set2.cc \
<snip>
	  

	Note
	The longish file list can be generated with: find ./ -iname \*.cc -printf '%P \\ \n'

Create autogen.sh:

! /bin/sh

aclocal \
&& automake --add-missing \
&& autoconf