The problem I am addressing is that of writing and building a Perl module in such a way that it builds and installs using both CPAN and Debian packaging.

On Ubuntu you will want the packages libmodule-starter-perl, dh-make and dh-make-perl. These will provide commands module-starter, dh_make and dh-make-perl. Note the variable use of hyphens and underscores!

The wrinkles occur because CPAN and Debian handle configuration files differently. I assume that the configuration files are going to be installed in /etc/$ProjectName.

Add the following at the end of your Makefile.PL, assuming you are using Module::Install.

package MY;
 
sub postamble {
     return << "EOF";
INST_ETC        = blib/etc
DESTINSTALLETC = \$(DESTDIR)/etc
# This target is used by both CPAN and Debian builds
config::
        $(MKPATH) $(INST_ETC)
 
# This target is used by both CPAN and Debian builds
pure_all::
	$(CP) -r etc/* $(INST_ETC)
 
# This target is used only by CPAN builds; Debian uses debian/conffiles
pure_install:: all
        $(MKPATH) $(DESTINSTALLETC)/$(NAME)
        $(CP) -r $(INST_ETC)/* $(DESTINSTALLETC)/$(NAME)
 
EOF
}

This will deal with installing things correctly when you do a 'make install'. In this fragment the DESTINSTALLETC macro defines where you ultimately want things installed.

Unfortunately, the Debian system does not use 'make install', not even with a fake root or over-rides to DESTDIR. To deal with Debian packaging you need a debian/conffiles in the project directory. This should list the source files, normally living in the etc directory, e.g

etc/log4perl.conf
etc/sessiontimewatcher.conf
etc/sql/schema.sql
etc/sql/test.sql

Now, the following script, run from one level above the project directory will build a Debian package for you

#!/bin/bash -xe

# Script to build a Perl module for Debian.
# Before running this script you must have created debian/control
# and debian/conffiles in the module's directory. debian/control
# will get created automatically the first time that you run this
# script, you can then edit it to suit. debian/conffiles you have
# to create yourself.

export DEB_BUILD_OPTIONS=nocheck
if [ ! -d $1 ]; then
    module-starter --module=$1 --mi --author='A N Other' \
        --email=nobody@example.com
fi
cd $1
if [ -f Makefile ]; then
    make distclean
else
    perl Makefile.PL
fi
cd ..
dh-make-perl --notest --noinstall --version 7 --verbose $1
cd $1
debuild -d -us -uc