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I & my colleagues store our .Net project using dropbox but it is very ugly to see the 'obj'/'bin' folder also sync to the internet.

We need to get rid of those folder when sync. How can we do that?

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There's a feature in new(er) builds of Dropbox called Selective sync. I think you need at least version 1.0. If you're not sure then just grab the latest stable release from here

Selective sync allows you to choose the folders you want synced to your computer. It gives you the ability to have more control over what is synced to your devices. It is particularly useful for users with limited hard drive space on one of the computers or netbooks synced to their Dropbox account.

So you're still syncing everything to your Dropbox account but you can select what you sync "back" to your computer(s)

There'a nice walkthrough with screenshots at How-to Geek

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