Thanks for the tips and the guidance.  I followed your advice and finally mi
files were:

configure.ac:
AC_INIT([hmi], [0.3], [EMAIL PROTECTED])
AM_INIT_AUTOMAKE([-Wall -Werror foreign])
AC_PROG_CXX
AC_CONFIG_FILES([
   Makefile
   src/Makefile
    ])
AC_OUTPUT

Makefile.am:
SUBDIRS = src

src/Makefile.am:
elementos =    \
   main.cpp \
   Base/AlarmManager.cpp  \
   Base/AlarmsSummary.cpp \
   Base/Container.cpp  \
   Base/HMIManager.cpp  \
   Base/Named.cpp  \
   Base/Object.cpp  \
   Base/Screen.cpp  \
   Base/Titled.cpp  \
   Base/Viewer.cpp  \
   Base/Window.cpp

bin_PROGRAMS = hmi
hmi_SOURCES =         \
   $(elementos)

AM_CXXFLAGS = -I/usr/include/libglademm-2.4 -I/usr/lib/libglademm-2.4/include
-I/usr/include/gtkmm-2.4 -I/usr/lib/gtkmm-2.4/include
-I/usr/include/libglade-2.0 -I/usr/include/glibmm-2.4
-I/usr/lib/glibmm-2.4/include
-I/usr/include/gdkmm-2.4 -I/usr/lib/gdkmm-2.4/include
-I/usr/include/pangomm-1.4 -I/usr/include/atkmm-1.6
-I/usr/include/gtk-2.0-I/usr/include/sigc++-
2.0 -I/usr/lib/sigc++-2.0/include -I/usr/include/glib-2.0 -I/usr/lib/glib-
2.0/include -I/usr/lib/gtk-2.0/include
-I/usr/include/cairomm-1.0-I/usr/include/pango-
1.0 -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/atk-1.0 -I/usr/include/libxml2
AM_LDFLAGS = -lglademm-2.4 -lglade-2.0 -lxml2 -lgtkmm-2.4 -lgdkmm-2.4 -
latkmm-1.6 -lgtk-x11-2.0 -lpangomm-1.4 -lcairomm-1.0 -lglibmm-2.4 -lsigc-2.0-
lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lm -lpangocairo-1.0 -lfontconfig
-lXext -lXrender -lXinerama -lXi -lXrandr -lXcursor -lXfixes
-lpango-1.0-lcairo -lX11 -
lgobject-2.0 -lgmodule-2.0 -ldl -lglib-2.0

When I issue "make" the project starts to compile but the .o files are being
thrown on "src/".  In the other subdirs from src/ there are files with
identical names to the .o files being generated.  I fear they will be
overwritten.

I been searching for more examples on compiling a project as this one with
source files in other subdirs but haven't been able to find any.   Can
anyone guide me towards solving this problem?

Thanks ...

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