Packages are zip files created inside the CQ5 that allows you to quickly create backups or copy entire websites or projects.
Go to "Package manager" on your start page, create a new one, add filters into (for every website I create, I package the content, design, apps and dam folders).
Later, on another CQ instance, go to Package manager again, upload your package and install it.
Take a look there http://dev.day.com/docs/en/cq/current/administering/package_manager.html for the extensive version and more details.
After looking again at the example I followed, and the package manager, I did see that this seems to be the way things are kept together.
One of the questions early on when looking at sling and jcr was not that I didn't understand the concepts they employ, but that the intelligence was in the layer above that in how all the pieces placed in the jcr using sling are put together to form a 'solution'. Like DNA, which only has 4 chemical building blocks: I "get" the chemicals and the double helix, but how do you get 'human' vs 'snail'. Understanding that is where the brilliance, beauty, intelligence, innovation, mystery lies.
So 'packages' managed by the package manager then is the technology piece that keeps all the pieces that belong to a 'solution' (eg website) together. Normally they can be scattered about in the jcr (/content, /etc, /lib, /apps, ...), but the package defines all these scattered pieces into one unit that can be copied, moved, exported, imported, etc. Right?
More or less.
What keep all these files, nodes, classes, OSGI bundles, jsp pages, whatever; is the reference that one file makes to another.
For example, you templates have a reference to the page component, and inside the code you get the references to the images, css files and other scripts. The design also have a reference, and the websites showed in the websites modules are the contentPages that have templates and designs together.
The packages only zip all these files and record the path to each one.
Please mark helpfull or correct if this helped you