magento - where did theme-related files and folders inside includes/src come from? - magento

New to Magento here, please bear with me.
I installed a theme on Magento, which has these folders: app, js, skin, which is the usual. However, when I tried to uninstall the theme, I found that there files and folders for the theme have been created inside includes/src folder. Where did they come from, when the downloaded zip file of the theme didn't contain them?
I noticed this only happens to some themes installed. I know the files are related to the theme because the folder names inside includes/src are the developer and theme names.
Any ideas?
Magento (Enterprise 1.12)

When you enable your compilation, Magento gets all the class and compiles them and puts them in includes/src directory. You can see all of your classes sitting there if you have your compilation on.
Check this in-depth details on Compilation by Alan Storm:
http://alanstorm.com/magento_compiler_path

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Cheers,
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I do disagree with the solution of Mr Storm.
ref: http://www.magentocommerce.com/knowledge-base/entry/magentos-theme-hierarchy
Those documents recommend You avoid to use the package default (as the base package too)
You have to creating Your own package 'mytheme' and to define a theme 'default'
ref: http://info.magento.com/rs/magentocommerce/images/MagentoDesignGuide.pdf
"Please ignore legacy Magento instructions and tutorials that instruct
you to create your custom theme inside of the default design package,
or to edit files in the default/default directory directly.
Rather,
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most protection from accidental changes is to create a new designpackage
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app/design/frontend/your-package/default
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app/design/frondend/default/your-theme
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app/design/frontend/default/mytheme
Then, in the admin go to
System -> Configuration -> Design
and enter mytheme in the Default field. Your theme will now the the "default" place Magento looks for files. If it doesn't find one, it will fall back on what it finds in the base folder.

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