While playing with add layers, I ended up add meta-rt twice which lead to meta-rt show up twice in the hob layer list, but only one entry is added in the bblayers.conf, which is correct
http://git.yoctoproject.org/cgit/cgit.cgi/poky/commit/?id=9cf5190679f372da212cbbbf85e27b9ea6a395f4
verified against latest master (commit 981052592b9157ee54a9971d36de33ac72fc6626)