I'm really not sure that changing the warning alone is sufficient.
Regardless of the -y option, I would prefer that apt not ask for
confirmation before downloading the repository source.  There are
several use cases that are improved by using the repository source, as
follows:

1) A Ubuntu developer wishes to work on source maintained in a VCS in
Debian.  In this case, the use of the VCS version may not be correct at
all, as there may be many changes to the source in the repositories that
are not reflected in the VCS.  This issue is compounded for Ubuntu
derivatives, where neither the Debian nor Ubuntu VCS may be correct.

2) The downloader is interested in understanding how a feature is
implemented, or reviewing the code for some other purpose.  In this
case, the use of the VCS is likely irrelevant, unless the downloader has
some reason why they would prefer the VCS, happens to have the
appropriate VCS tools installed, and needs to see the very latest code
for some reason.

3) A Debian developer wishes to download Ubuntu source to review the
specific changes made in more detail than is obvious from
patches.ubuntu.com, when the Debian developer uses a VCS to manage the
package.  In this case, the warning is definitely not correct, as the
specific changes in which the downloader is interested are certainly not
in the VCS.

4) A new developer is interested in preparing a patch to be sent
upstream for their pet feature, and the repositories carry the latest
upstream version.  In this case, a pointer to the VCS for the packaging
is largely unimportant, as the developer is interested only in the
upstream code.  It may be that this person should visit the upstream
VCS, but this may be daunting for beginners.

5) A user is required to recompile to enable some compile-time option as
indicated in the documentation.  Such user may well be an LTS user, and
so the VCS maintained version may not be appropriate (especially if the
package maintainer does not branch at each upload).

6) A user has encountered a behavioral change in the package, and wishes
to understand the differences between two versions.  For such a user,
redirection to the VCS may require review of significantly more output
(which may be less obvious to generate) than using versioned apt-get
(e.g. apt-get source myfavoritepackage=5.3.6-3ubuntu14) and debdiff.

Contrariwise, I believe the only use case improved by stopping to ask is
that an Ubuntu developer working on a package maintained in an Ubuntu
VCS is notified that changes should be committed to the VCS rather than
uploaded blindly.

-- 
Version control system warnings intrusive and unclear
https://bugs.launchpad.net/bugs/129575
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