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Unlike web browsers, the CA root cert is not installed by default for svn clients. You would need to tell the client where to find it in order to trust the ssl cert.

Reference: svnbook

For GoDaddy signed certs, download their root certs available at:

http://certificates.godaddy.com/repository

You would need both the pem encoded gd-class2-root.crt and gd_intermediate.crt .

Then in subversion client global settings, tell it the path to the certs:

This should then trust the ssl cert.