Starting from 0.9.0 RC2 configuration file is located in another location.

~/.config/robomongo/0.9/robomongo.json

For 0.9.0 RC1 and below versions config file located here:

~/.config/robomongo/robomongo.json

To migrate your old connection stirngs to the new version, just copy 0.9 folder and all your connections will be restored:

$ cp ~/.config/robomongo/robomongo.json ~/.config/robomongo/0.9/robomongo.json

Read more details in our blog post: https://blog.robomongo.org/robomongo-rc2-for-windows-mac-os-x-and-linux/