I got the solution, which is very sloppy indeed. I had to edit the settings file in /Users/XXX/Library/Preferences/SAP/ and add two lines:
@INCLUDE = file:///Users/joaosousa/Library/Preferences/SAP/connections
@MESSAGESERVER = file:///Users/joaosousa/Library/Preferences/SAP/messageservers.txt
I also had to create a dummy messageservers.txt which has garbage inside, so that Eclipse doesn't throw an error.
Why can't Eclipse just use the connections of SAP Logon instead of wasting everyone's time, forcing us to create dummy files and manually edit configuration files? Sloppy (let me just say it.... LAZY) development on SAP's behalf.