I’m using a build system like so:

{
	"variants":
	
		{
			"name": "test",
			"working_dir": "$project_path",
			"cmd": "builder", "--args"]
		}
	]
}

ctrl+shift+p t enter
In ST2 this worked fine. Now in ST3 it’s using the directory of whatever source file I have active at the time. As a workaround I bring some file in the project folder to the foreground.