(debian-policy.info)Changes to the upstream sources

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4.3 Changes to the upstream sources
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If changes to the source code are made that are not specific to the
needs of the Debian system, they should be sent to the upstream authors
in whatever form they prefer so as to be included in the upstream
version of the package.

If you need to configure the package differently for Debian or for
Linux, and the upstream source doesn’t provide a way to do so, you
should add such configuration facilities (for example, a new ‘autoconf’
test or ‘#define’) and send the patch to the upstream authors, with the
default set to the way they originally had it.  You can then easily
override the default in your ‘debian/rules’ or wherever is appropriate.

You should make sure that the ‘configure’ utility detects the correct
architecture specification string (refer to Note: Architecture
specification strings. for details).

If your package includes the scripts ‘config.sub’ and ‘config.guess’,
you should arrange for the versions provided by the package
autotools-dev be used instead (see autotools-dev documentation for
details how to achieve that).  This ensures that these files can be
updated distribution-wide at build time when introducing new
architectures.

If you need to edit a ‘Makefile’ where GNU-style ‘configure’ scripts are
used, you should edit the ‘.in’ files rather than editing the ‘Makefile’
directly.  This allows the user to reconfigure the package if necessary.
You should `not' configure the package and edit the generated
‘Makefile’!  This makes it impossible for someone else to later
reconfigure the package without losing the changes you made.