I have created a cloud app, with a distributed packaged that makes azure download the content from a weburl. (composite c1)
Now i would like to take a backup of my application, possible do some changes to the source code and upload again.
How can i get a backup of the files on the cloudapp?
You aren't very clear if you need a backup of your application code, or the files that are being downloaded (though I think you somewhat clarify in your follow up comment).
When you deploy a Cloud Services app the code is packaged into the cspkg file and sent up to be deployed. Some of the deployment tools (like Visual Studio, the PowerShell Cmdlets, etc.) will use a storage account to upload the package file to BLOB storage. This means that you'd have a copy of the packages you've deployed. If you don't use a tool that uses the storage account to deploy from I highly recommend you also keep a copy of the packages you deploy just in case you need to roll back to one.
Now, if you are changing code in your application, then you make the change locally, test it out and then you can redploy. You have several options for this. You can delete the previous deployment and redeploy the new one (which will cause downtime for your app). Another option is to do an inplace upgrade where your deployment is updated with the new package a few machines at a time (if you are running multiple instances). The other options is also a VIP swap where you load up your new code in the staging slot and then swap the bits between staging and production. I'd suggest researching these options to deploy new code on MSDN to understand them (they all have benefits and drawbacks, and some of them can't be done depending on the changes you are making to your code).
In your comment it seems that you are more interested in getting a back up of the files that are in your BLOB storage account after you application pulls them down. You have a couple of opions here as well: