I've been able to study 5 Magento shops in the last weeks. And I've noticed a mess in module management.

I've seen 2 places where the modules/extensions appear:

- MagentoConnect page: where you can see the module name, description, version and you are able to uninstall or upgrade
- /app/etc/modules directory: where the main XML of the module appear

My questions about modules:

1) Why do I see some modules appearing in "etc" directory, but they don't appear in MagentoConnect page ?

2) In that cases, how can I uninstall a module?

3) And how can I know which files are related with that module ?

Thank you !