Set custom keyboard mapping

I'm using Xubuntu. I'm not sure if this applies to other flavors of Ubuntu as well.

I used to set a custom keyboard mapping in .XCompose.

# Include systemwide config
include "%L"

<Multi_key> <colon> <3>                 : "?"       # : 3   Panda
<Multi_key> <8> <period>                : "☃"       # 8 .   Snowman
<Multi_key> <equal> <parenright>        : "?"       # = ) grinning cat face with smiling eyes
<Multi_key> <equal> <minus>             : "?"       # = - cat face with tears of joy
<Multi_key> <equal> <D>                 : "?"       # = D smiling cat face with open mouth
<Multi_key> <equal> <3>                 : "?"       # = 3 smiling cat face with heart-shaped eyes
<Multi_key> <equal> <slash>             : "?"       # = / cat face with wry smile
<Multi_key> <bar> <3>                   : "?"       # | 3 kissing cat face with closed eyes
<Multi_key> <greater> <equal>           : "?"       # > 3 pouting cat face
<Multi_key> <equal> <parenleft>         : "?"       # = ( crying cat face
<Multi_key> <D> <equal>                 : "?"       # D = weary cat face
<Multi_key> <p> <p>                     : "?"       # p p pumpkin

This can be loaded by setting xim as input method using im-config. This still works, but not always. It doesn't work in Atom and as of <insert the breaking Ubuntu version here> it makes synapse crash entirely.

I've also read at some point that .XModmap is deprecated, but I don't recall the exact sources.

All sources on what to configure exactly are a big vague. The only thing I got to work is using .XModmap.

What is the way to go nowadays (Xubuntu 16.04 / 16.10) to set custom key mappings? Preferably system-wide.