Build: Get build system in order

Makefile.am

@@ -1,16 +1,5 @@
 SUBDIRS = corelogic
 
-AM_CPPFLAGS = -I$(srcdir)/corelogic/include
-
 bin_PROGRAMS = harikoff
 harikoff_SOURCES = main.cpp
 harikoff_LDADD = corelogic/libcorelogic.a
-
-# List of static miscellaneous files to include in the distribution
-EXTRA_DIST = \
-    COPYING \
-    README \
-    ChangeLog \
-    AUTHORS \
-    INSTALL \
-    NEWS

configure.ac

@@ -1,12 +1,14 @@
-AC_INIT([The Harriman-Peikoff Project], [0.00], [latentprion@gmail.com], 
-    [harikoff], [github.com/latentprion/harikoff])
+AC_INIT([The Harriman-Peikoff Project], [0.00.000],
+    [latentprion@gmail.com],
+    [harikoff],
+    [github.com/latentprion/harikoff])
 
 # Safety checks in case user overwritten --srcdir
 AC_CONFIG_SRCDIR([corelogic/mind.cpp])
 
 # Store the auxiliary build tools (e.g., install-sh, config.sub, config.guess)
 # in this dir (build-aux)
-AC_CONFIG_AUX_DIR([build-aux])
+AC_CONFIG_AUX_DIR([autotools-aux])
 
 # Init automake, and specify this program does not follow the gnu coding standards.
 AM_INIT_AUTOMAKE([foreign -Wall -Werror])
@@ -16,7 +18,13 @@ AC_PROG_CXX
 AC_PROG_RANLIB
 AM_PROG_AR
 
-AC_CONFIG_HEADERS([config.h])
+AM_CPPFLAGS="-I\"\$(abs_top_srcdir)/include\" -I\"\$(abs_top_srcdir)/corelogic/include\""
+
+AC_SUBST(AM_CPPFLAGS)
+
+AC_CONFIG_HEADERS([include/config.h])
+AC_CONFIG_FILES([
+    Makefile corelogic/Makefile
+])
 
-AC_CONFIG_FILES([Makefile corelogic/Makefile])
 AC_OUTPUT

corelogic/Makefile.am

@@ -1,4 +1,2 @@
-AM_CPPFLAGS = -I$(srcdir)/include
-
 noinst_LIBRARIES = libcorelogic.a
 libcorelogic_a_SOURCES = painfulQuale.cpp mind.cpp