Store run configuration with project in Eclipse

Yes - open "Run" then "Run Configurations...", and select your configuration. Click on the last tab, "Common". Under "Save As", choose "Shared File" instead of "Local File".

This dialog is a little confusing. The line next to "Shared File" can only be a path, not a file name - and it defaults to the root path of the current project. Once you hit "Apply", a file named the [Run Configuration Name] + ".launch" is created within that folder. So in my above example, this results in a "/JavaTest/JavaTest.launch" file. This is something that can be comitted to version control.