The program quilt offers a basic method for recording modifications to the upstream source for Debian packaging. It's useful to have a slightly customized default, so let's create an alias dquilt for Debian packaging by adding the following line to ~/.bashrc.

alias dquilt="quilt --quiltrc=${HOME}/.quiltrc-dpkg"

Then let's create ~/.quiltrc-dpkg as follows.

d=. ; while [ ! -d $d/debian -a `readlink -e $d` != / ]; do d=$d/..; done
if [ -d $d/debian ] && [ -z $QUILT_PATCHES ]; then
    # if in Debian packaging tree with unset $QUILT_PATCHES
    QUILT_PATCHES="debian/patches"
    QUILT_PATCH_OPTS="--reject-format=unified"
    QUILT_DIFF_ARGS="-p ab --no-timestamps --no-index --color=auto"
    QUILT_REFRESH_ARGS="-p ab --no-timestamps --no-index"
    QUILT_COLORS="diff_hdr=1;32:diff_add=1;34:diff_rem=1;31:diff_hunk=1;33:diff_ctx=35:diff_cctx=33"
    if ! [ -d $d/debian/patches ]; then mkdir $d/debian/patches; fi
fi

See quilt(1) and /usr/share/doc/quilt/quilt.pdf.gz on how to use quilt.

Let's assume you find an error in the upstream Makefile as follows where install: gentoo should have been install: gentoo-target.

install: gentoo
        install ./gentoo $(BIN)
        install icons/* $(ICONS)
        install gentoorc-example $(HOME)/.gentoorc

Let's fix this and record it with the dquilt command as fix-gentoo-target.patch. ^[22]

$ mkdir debian/patches
$ dquilt new fix-gentoo-target.patch
$ dquilt add Makefile

You change the Makefile file as follows.

install: gentoo-target
        install ./gentoo $(BIN)
        install icons/* $(ICONS)
        install gentoorc-example $(HOME)/.gentoorc

Ask dquilt to generate the patch to create debian/patches/fix-gentoo-target.patch and add its description following DEP-3: Patch Tagging Guidelines.

$ dquilt refresh
$ dquilt header -e
... describe patch

Most third-party software installs itself in the /usr/local directory hierarchy. On Debian this is reserved for private use by the system administrator, so packages must not use directories such as /usr/local/bin but should instead use system directories such as /usr/bin, obeying the Filesystem Hierarchy Standard (FHS).

Normally, make(1) is used to automate building the program, and executing make install installs programs directly to the desired destination (following the install target in the Makefile). In order for Debian to provide pre-built installable packages, it modifies the build system to install programs into a file tree image created under a temporary directory instead of the actual destination.

These two differences between normal program installation on one hand and the Debian packaging system on the other can be transparently addressed by the debhelper package through the dh_auto_configure and dh_auto_install commands if the following conditions are met.

Programs that use GNU autoconf follow the GNU conventions automatically, so they can be trivial to package. On the basis of this and other heuristics, it is estimated that the debhelper package will work for about 90% of packages without making any intrusive changes to their build system. So packaging is not as complicated as it may seem.

If you need to make changes in the Makefile, you should be careful to support the $(DESTDIR) variable. Although it is unset by default, the $(DESTDIR) variable is prepended to each file path used for the program installation. The packaging script will set $(DESTDIR) to the temporary directory.

For a source package generating a single binary package, the temporary directory used by the dh_auto_install command will be set to debian/package. ^[24] Everything that is contained in the temporary directory will be installed on users' systems when they install your package; the only difference is that dpkg will be installing the files to paths relative to the root directory rather than your working directory.

Bear in mind that even though your program installs in debian/package, it still needs to behave correctly when installed from the .deb package under the root directory. So you must not allow the build system to hardcode strings like /home/me/deb/package-version/usr/share/package into files in the package.

Here's the relevant part of gentoo's Makefile^[25]:

# Where to put executable commands on 'make install'?
BIN     = /usr/local/bin
# Where to put icons on 'make install'?
ICONS   = /usr/local/share/gentoo

We see that the files are set to install under /usr/local. As explained above, that directory hierarchy is reserved for local use on Debian, so change those paths to:

# Where to put executable commands on 'make install'?
BIN     = $(DESTDIR)/usr/bin
# Where to put icons on 'make install'?
ICONS   = $(DESTDIR)/usr/share/gentoo

The exact locations that should be used for binaries, icons, documentation, etc. are specified in the Filesystem Hierarchy Standard (FHS). You should browse through it and read the sections relevant to your package.

So, we should install executable commands in /usr/bin instead of /usr/local/bin, the manual page in /usr/share/man/man1 instead of /usr/local/man/man1, and so on. Notice how there's no manual page mentioned in gentoo's Makefile, but since Debian Policy requires that every program has one, we'll make one later and install it in /usr/share/man/man1.

Some programs don't use Makefile variables to define paths such as these. This means you might have to edit some real C sources in order to fix them to use the right locations. But where to search, and exactly what for? You can find this out by issuing:

$ grep -nr --include='*.[c|h]' -e 'usr/local/lib' .

grep will run recursively through the source tree and tell you the filename and the line number for all matches.

Edit those files and in those lines replace usr/local/lib with usr/lib. This can be done automatically as follows:

$ sed -i -e 's#usr/local/lib#usr/lib#g' \
        $(find . -type f -name '*.[c|h]')

If you want to confirm each substitution instead, this can be done interactively as follows:

$ vim '+argdo %s#usr/local/lib#usr/lib#gce|update' +q \
        $(find . -type f -name '*.[c|h]')

Next you should find the install target (searching for the line that starts with install: will usually work) and rename all references to directories other than ones defined at the top of the Makefile.

Originally, gentoo's install target said:

install: gentoo-target
        install ./gentoo $(BIN)
        install icons/* $(ICONS)
        install gentoorc-example $(HOME)/.gentoorc

Let's fix this upstream bug and record it with the dquilt command as debian/patches/install.patch.

$ dquilt new install.patch
$ dquilt add Makefile

In your editor, change this for the Debian package as follows:

install: gentoo-target
        install -d $(BIN) $(ICONS) $(DESTDIR)/etc
        install ./gentoo $(BIN)
        install -m644 icons/* $(ICONS)
        install -m644 gentoorc-example $(DESTDIR)/etc/gentoorc

You'll have noticed that there's now an install -d command before the other commands in the rule. The original Makefile didn't have it because usually /usr/local/bin and other directories already exist on the system where you are running make install. However, since we will be installing into a newly created private directory tree, we will have to create each and every one of those directories.

We can also add in other things at the end of the rule, like the installation of additional documentation that the upstream authors sometimes omit:

        install -d $(DESTDIR)/usr/share/doc/gentoo/html
        cp -a docs/* $(DESTDIR)/usr/share/doc/gentoo/html

Check carefully, and if everything is okay, ask dquilt to generate the patch to create debian/patches/install.patch and add its description.

$ dquilt refresh
$ dquilt header -e
... describe patch

Now you have a series of patches.

Whenever you make changes that are not specific to the Debian package such as debian/patches/fix-gentoo-target.patch, be sure to send them to the upstream maintainer so they can be included in the next version of the program and be useful to everyone else. Also remember to avoid making your fixes specific to Debian or Linux - or even Unix! Make them portable. This will make your fixes much easier to apply.

Note that you don't have to send the debian/* files upstream.

There is one other common problem: libraries are often different from platform to platform. For example, a Makefile can contain a reference to a library which doesn't exist on the Debian system. In that case, we need to change it to a library which does exist in Debian, and serves the same purpose.

Let's assume a line in your program's Makefile (or Makefile.in) as the following.

LIBS = -lfoo -lbar

If your program doesn't compile since the foo library doesn't exist and its equivalent is provided by the foo2 library on the Debian system, you can fix this build problem as debian/patches/foo2.patch by changing foo into foo2.^[26]

$ dquilt new foo2.patch
$ dquilt add Makefile
$ sed -i -e 's/-lfoo/-lfoo2/g' Makefile
$ dquilt refresh
$ dquilt header -e
... describe patch