Changes to the build system to update the autoconf files, introduce a proper

build system for doc/ and remove all generated files and symbolic links.
Also private headers so that the distribution tarball builds.
Use gnu standards (COPYING, README, NEWS, ChangeLog) globally, no need to
specify in each Makefile.

.gitignore

-# http://www.gnu.org/software/automake
+*~
 
+Makefile
 Makefile.in
-
-# http://www.gnu.org/software/autoconf
+INSTALL
+config.guess
+config.h
+config.status
+config.h.in
+config.sub
+ltmain.sh
+libtool
+
+doc/doxyfile.stamp
+doc/html/
+doc/latex/
+doc/man/
+doc/Doxyfile
+
+examples/test
+examples/test_bh
+examples/test_bh_sorted
+examples/test_fmm_sorted
+examples/test_qr
+
+m4/libtool.m4
+m4/ltoptions.m4
+m4/ltsugar.m4
+m4/ltversion.m4
+m4/lt~obsolete.m4
 
 /autom4te.cache
 /aclocal.m4
@@ -12,7 +37,9 @@ Makefile.in
 /install-sh
 /missing
 /stamp-h1
+
 # Object files
+.deps/
 *.o
 *.ko
 *.obj
@@ -147,3 +174,4 @@ sympy-plots-for-*.tex/
 
 # xindy
 *.xdy
+

COPYING

-/usr/share/automake-1.11/COPYING
\ No newline at end of file

INSTALL

-/usr/share/automake-1.11/INSTALL
\ No newline at end of file

Makefile.am

@@ -16,7 +16,6 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 # Automake stuff
-AUTOMAKE_OPTIONS = gnu
 ACLOCAL_AMFLAGS = -I m4
 
 # Show the way...

autogen.sh

 #! /bin/sh
-# autogen.sh
 
-# This file is part of GadgetSMP.
-# Coypright (c) 2012 pedro.gonnet@durham.ac.uk.
-# 
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-# 
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-# 
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#  Update generated configuration files, i.e. do work so that a
+#  developer checkout can be configured.
 
-# make libtool and stuff
-libtoolize --force --copy
+autoreconf --install --symlink 
 
-# run aclocal
-aclocal -I m4/
-
-# run autoconf
-autoconf -I m4
-
-# run autoheader to generate config.h.in
-autoheader -I m4
-
-# run automake
-automake --add-missing
+exit
 

compile

-/usr/share/automake-1.11/compile
\ No newline at end of file

config.guess

-/usr/share/automake-1.11/config.guess
\ No newline at end of file

config.h.in

-/* config.h.in.  Generated from configure.ac by autoheader.  */
-
-/* Support AVX (Advanced Vector Extensions) instructions */
-#undef HAVE_AVX
-
-/* Define to 1 if you have the `clock_gettime' function. */
-#undef HAVE_CLOCK_GETTIME
-
-/* Define to 1 if you have the <c_asm.h> header file. */
-#undef HAVE_C_ASM_H
-
-/* Define to 1 if you have the <dlfcn.h> header file. */
-#undef HAVE_DLFCN_H
-
-/* Define to 1 if you have the `gethrtime' function. */
-#undef HAVE_GETHRTIME
-
-/* Define to 1 if hrtime_t is defined in <sys/time.h> */
-#undef HAVE_HRTIME_T
-
-/* Define to 1 if you have the <intrinsics.h> header file. */
-#undef HAVE_INTRINSICS_H
-
-/* Define to 1 if you have the <inttypes.h> header file. */
-#undef HAVE_INTTYPES_H
-
-/* Define to 1 if you have the `mach_absolute_time' function. */
-#undef HAVE_MACH_ABSOLUTE_TIME
-
-/* Define to 1 if you have the <mach/mach_time.h> header file. */
-#undef HAVE_MACH_MACH_TIME_H
-
-/* Define to 1 if you have the <memory.h> header file. */
-#undef HAVE_MEMORY_H
-
-/* Support MMX instructions */
-#undef HAVE_MMX
-
-/* Define if OpenMP is enabled */
-#undef HAVE_OPENMP
-
-/* Define to 1 if `posix_memalign' works. */
-#undef HAVE_POSIX_MEMALIGN
-
-/* Define if you have POSIX threads libraries and header files. */
-#undef HAVE_PTHREAD
-
-/* Define to 1 if you have the `read_real_time' function. */
-#undef HAVE_READ_REAL_TIME
-
-/* Support SSE (Streaming SIMD Extensions) instructions */
-#undef HAVE_SSE
-
-/* Support SSE2 (Streaming SIMD Extensions 2) instructions */
-#undef HAVE_SSE2
-
-/* Support SSE3 (Streaming SIMD Extensions 3) instructions */
-#undef HAVE_SSE3
-
-/* Support SSE4.1 (Streaming SIMD Extensions 4.1) instructions */
-#undef HAVE_SSE41
-
-/* Support SSE4.2 (Streaming SIMD Extensions 4.2) instructions */
-#undef HAVE_SSE42
-
-/* Support SSSE3 (Supplemental Streaming SIMD Extensions 3) instructions */
-#undef HAVE_SSSE3
-
-/* Define to 1 if you have the <stdint.h> header file. */
-#undef HAVE_STDINT_H
-
-/* Define to 1 if you have the <stdlib.h> header file. */
-#undef HAVE_STDLIB_H
-
-/* Define to 1 if you have the <strings.h> header file. */
-#undef HAVE_STRINGS_H
-
-/* Define to 1 if you have the <string.h> header file. */
-#undef HAVE_STRING_H
-
-/* Define to 1 if you have the <sys/stat.h> header file. */
-#undef HAVE_SYS_STAT_H
-
-/* Define to 1 if you have the <sys/time.h> header file. */
-#undef HAVE_SYS_TIME_H
-
-/* Define to 1 if you have the <sys/types.h> header file. */
-#undef HAVE_SYS_TYPES_H
-
-/* Define to 1 if you have the `time_base_to_time' function. */
-#undef HAVE_TIME_BASE_TO_TIME
-
-/* Define to 1 if you have the <unistd.h> header file. */
-#undef HAVE_UNISTD_H
-
-/* Define if you have the UNICOS _rtc() intrinsic. */
-#undef HAVE__RTC
-
-/* Define to the sub-directory in which libtool stores uninstalled libraries.
-   */
-#undef LT_OBJDIR
-
-/* Define to 1 if your C compiler doesn't accept -c and -o together. */
-#undef NO_MINUS_C_MINUS_O
-
-/* Name of package */
-#undef PACKAGE
-
-/* Define to the address where bug reports for this package should be sent. */
-#undef PACKAGE_BUGREPORT
-
-/* Define to the full name of this package. */
-#undef PACKAGE_NAME
-
-/* Define to the full name and version of this package. */
-#undef PACKAGE_STRING
-
-/* Define to the one symbol short name of this package. */
-#undef PACKAGE_TARNAME
-
-/* Define to the version of this package. */
-#undef PACKAGE_VERSION
-
-/* Define to necessary symbol if this constant uses a non-standard name on
-   your system. */
-#undef PTHREAD_CREATE_JOINABLE
-
-/* Define to 1 if you have the ANSI C header files. */
-#undef STDC_HEADERS
-
-/* Define to 1 if you can safely include both <sys/time.h> and <time.h>. */
-#undef TIME_WITH_SYS_TIME
-
-/* Enable extensions on AIX 3, Interix.  */
-#ifndef _ALL_SOURCE
-# undef _ALL_SOURCE
-#endif
-/* Enable GNU extensions on systems that have them.  */
-#ifndef _GNU_SOURCE
-# undef _GNU_SOURCE
-#endif
-/* Enable threading extensions on Solaris.  */
-#ifndef _POSIX_PTHREAD_SEMANTICS
-# undef _POSIX_PTHREAD_SEMANTICS
-#endif
-/* Enable extensions on HP NonStop.  */
-#ifndef _TANDEM_SOURCE
-# undef _TANDEM_SOURCE
-#endif
-/* Enable general extensions on Solaris.  */
-#ifndef __EXTENSIONS__
-# undef __EXTENSIONS__
-#endif
-
-
-/* Version number of package */
-#undef VERSION
-
-/* Define to 1 if on MINIX. */
-#undef _MINIX
-
-/* Define to 2 if the system does not provide POSIX.1 features except with
-   this defined. */
-#undef _POSIX_1_SOURCE
-
-/* Define to 1 if you need to in order for `stat' and other things to work. */
-#undef _POSIX_SOURCE
-
-/* Define to `__inline__' or `__inline' if that's what the C compiler
-   calls it, or to nothing if 'inline' is not supported under any name.  */
-#ifndef __cplusplus
-#undef inline
-#endif

config.sub

-/usr/share/automake-1.11/config.sub
\ No newline at end of file