So here are a couple of ways I've found to get around this limitation.
First option ... different svn client
Not optimal but you could use an external SVN client (like TortoiseSVN) instead of the eclipse SVN client. Not the ideal solution but since Tortoise and the eclipse SVN clients use the same SVN config files you can use the built in client to check in your src folder and only use Tortoise to check in the output folder.
A Second option... eclipse external program xcopy
Create another folder say bin-checkin in your project then create an external tool configuration in eclipse to copy the data over.... (Run -> External Tools menu)
Location:
C:\windows\system32\xcopy.exe
Working Directory:
${workspace_loc:/temp/bin-debug}
Arguments:
*.* ${workspace_loc:/temp/bin-checkin} /e /y
You can then just run the external program from the menu to copy the data over
because this folder is not the output folder SVN will let you check it in.
Third option.... eclipse project Builder xcopy
(and this is the best because it's automatic)
do the same as the second option above but set it up as a builder instead of an external program This option is under builders in the project properties.
Here you use the same settings as above (using xcopy) you set it up on the main tab on the "Edit launch configuration properties" window, when you create a new Builder.
Once you've set that up you then switch to the Build Options tab in this same dialog and check the options you want such as "During manual builds" or "During auto builds", "After a clean" it depends on your preference. If you choose "During auto builds" make sure you click the "Specify Resources..." button and select your bin-debug folder. (this is the folder that will be monitored to detect when the auto build needs to be triggered)
Note: I've had best success setting the After a Clean, During manual, and During auto.
