Steps to reproduce the issue

1. Log into Joomla's Administrator Section.
2. Go to the Extension Manager.
3. Under "install" install "pkg_test_v1.zip" -> Success!
4. Now upgrade by installing "pkg_test_v101.zip" -> Warning Thrown.

Note: For sample Zip packages please see original bug report in the old bug tracker at: Bug Tracker {#34084}

Full Details

When installing a package over the top of an existing package that has a new entry in it's manifest the following error is thrown:

"JInstaller: :Install: Cannot find XML setup file" by libraries/cms/installer.php line ~1912

From what I can see normally the installer looks to the "tmp" directory for the xml files.
However with an update containing new packages the installer actually looks in the install location (e.g. plugins/system/plg_name) which doesn't exist yet as it hasn't been installed.

This issue occurs on update rather than on fresh installation of the package extension.

Reasons/Scenarios why I believe this is required logic:

1. You release a new version of your extension which contains a new feature (in the form of a plugin for example). You would expect to be able to install this package over the top of the existing record without receiving warning messages.

2. You have a free extension(package) & a commercial extension. The commercial extension includes extra plugins, modules etc. Users who upgrade their extension by installing the "pro" version over the "free" version will experience this issue.

Please see attached example for how to recreate this scenario.

Thanks for your time.

Additional Comments

This is a continuation from: http://joomlacode.org/gf/project/joomla/tracker/?action=TrackerItemEdit&tracker_item_id=34084