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for make mods simple:

for make simple mods folder (if you used pysch engine) you have to copie the template in : 
/mods
  base-game
  template.zip    -- not make yet

un-zip it and modified im, help you with the readme.md :].

for make full mods:

for make full mods (modifed the source code), you have to modifie the : 
/source
  assets/
  mods/
  scripts/  -- this
  ...

[!WARNING] can be hard to modifie, call me if you have any probleme.

or

modified the in mods script folder, more easy 
/myMods
  /scripts
    onGame.js
    onFreeplay.js
    ...

[!NOTE] if you want call a other script in use FMS_playScript("myScript","scripts/myLittleScript.js)

if you use the old version:

you have to use the source code use wapper HTML to exe