a few automake/autoconf deprecated

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Hello, when I run autogen.sh, I get this messages.
it would be nice to fix these old deprecated constructions

Cheers

Frederic

picca@mordor:~/Projets/coot$ ./autogen.sh 
libtoolize --copy --no-warn
aclocal -I macros
aclocal: warning: autoconf input should be named 'configure.ac', not 
'configure.in'
autoconf
automake --add-missing --copy
automake: warning: autoconf input should be named 'configure.ac', not 
'configure.in'
configure.in:31: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are 
deprecated.  For more info, see:
configure.in:31: 
http://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_
005fAUTOMAKE-invocation
automake: warning: autoconf input should be named 'configure.ac', not 
'configure.in'
analysis/Makefile.am:8: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
angles/Makefile.am:9: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')
auxil/catcheck/Makefile.am:4: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
auxil/rama/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
auxil/sec-str/Makefile.am:3: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
auxil/strand-analysis/Makefile.am:5: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
auxil/vectors/Makefile.am:3: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
build/Makefile.am:25: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')
ccp4mg-utils/Makefile.am:27: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
coords/Makefile.am:27: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
coot-surface/Makefile.am:21: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
coot-utils/Makefile.am:36: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
cootaneer/Makefile.am:23: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
cootilus/Makefile.am:23: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
db-main/Makefile.am:8: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
density-contour/Makefile.am:23: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
geometry/Makefile.am:27: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
goograph/Makefile.am:22: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
high-res/Makefile.am:29: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
ideal/Makefile.am:32: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')
lbg/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')
libgtkgraph/Makefile.am:2: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
lidia-core/Makefile.am:27: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
ligand/Makefile.am:26: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
mini-mol/Makefile.am:25: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
protein_db/Makefile.am:22: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
skeleton/Makefile.am:24: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
src/Makefile.am:183: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')
surface/Makefile.am:2: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
tw/Makefile.am:28: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')
utils/Makefile.am:21: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')

Original issue reported on code.google.com by pi...@synchrotron-soleil.fr on 8 Jun 2013 at 7:38

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Noted.  I plan to change to configure.ac in 0.8.

Original comment by pemsley@gmail.com on 2 Jul 2013 at 11:24

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Do you solve this issue at the end? (I have the same one)

Original comment by pietrod...@gmail.com on 5 Jun 2014 at 1:52

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(I have the same problem about 
"configure.ac:691: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')")

Original comment by pietrod...@gmail.com on 5 Jun 2014 at 1:53