Moved autoconf to root directory

.gitignore

@@ -16,3 +16,6 @@ makefile.dep
 /sourceme.sh
 /tmp
 /codes
+/config.*
+/autom4*
+

autoconf/.gitignore

-config.*
-autom4*
-Makefile.conf
-sourceme.sh
-test*

autoconf/README

-DO NOT EDIT configure FILE
-
-One should edit configure.ac and the run autoconf in this
-directory. Also the resulting "configure" is stored on the git,
-so as to allow people not to install a recent autoconf on their
-system.
-If you modify configure.ac, remember to run
-autoconf and then commit both files to the git repository.
-
-

autoconf/configure.ac → configure.ac

+# DO NOT EDIT ./configure FILE
+# One should edit configure.ac and the run autoconf in this
+# directory. Also the resulting "configure" is stored on the git,
+# so as to allow people not to install a recent autoconf on their
+# system.
+# If you modify configure.ac, remember to run
+# autoconf and then commit both files to the git repository.
+
 # we require a recent version
 # notice that autoconf is not necessary on user's machine, but only
 # if one has to update configure.ac
@@ -453,7 +461,7 @@ AC_MSG_NOTICE([**** To add a suffix to this name, set PLUMED_LIBSUFFIX environme
 
 
 AC_SUBST(build_dir)
-build_dir=`cd ../; pwd`
+build_dir=`pwd`
 
 # This is to replace tags in Makefile.conf.in
 # saving the result to Makefile.conf