In my development, once of the steps is to check the changes I made before I commit them.

To do so, I often use Meld.

Unfortunately, the preferences disappeared and it makes things harder to tweak large changes!

The fact is that my brain does not correctly support the Macintosh like Menu at the very top. (It's not just my brain, it's also the fact that when I move my mouse, it focuses windows automatically, which is the normal X-Windows behavior, and having the menus on the top is not acceptable in that case!)

You remove the menus at the top-right of the screen with:

sudo apt-get remove indicator-appmenu

The problem is that Meld uses that top-right menu for its preferences (among other things...) so I do not have access to those. Unfortunate.

Ah! But those preferences are Gnome preferences, so they are accessible through dconf-editor.

So... go to your console, start that tool as in:

dconf-editor

And then click on the following menu items:

org.gnome.meld

To get to the area where meld preferences are. When you click on "meld", you see the preferences on the right panel.

Just click, edit, whatnot and see what happens. The changes should take immediately. For example, you could display / hide the line numbers by clicking:

show-line-numbers

The lines will appear disappear depending on whether you see a checkmark.

Note that Meld may crash when you change certain things. It should auto-restart and may not close the old window. At least, I'm experiencing such problems every now and then.