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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:
0.9
$ cp ~/.config/robomongo/robomongo.json ~/.config/robomongo/0.9/robomongo.json
Read more details in our blog post: http://blog.robomongo.org/robomongo-rc2-for-windows-mac-os-x-and-linux/