I've been using Liclipse for a while, after having supported it in the IndieGogo funding drive a few years ago. However, there are a number of issues that I'm always hopping will get fixed in the next update, yet I haven't found any way to cleanly apply said updates.
The Help -> Check for Updates
menu doesn't ever show updates to LiClipse, which means the only way I've been able to do it is to download a new copy and overwrite my old one. Unfortunately, this breaks all my existing plugins, so I have to re-install said plugins, which is a petty annoying pain.
I'm using OSX El Capitan, which I think is why plugins get blown aaway upon update? They're all stored in the .app, which gets replaced entirely.