Yes, as @Schamper recommends, do not use relative paths to break out of the plugin's root directory, just use module.parent.require to require from the context of plugins.js, or require.main.require to require from the context of app.js
To answer OP, I use npm link to link my folders together. I have one big messy NodeBB install ( 😉 ) and next to it is a plugins/ folder where all the plugins live.
@psychobunny integrated grunt into NodeBB, so I just use grunt --verbose to develop now, instead of ./nodebb dev 😄
I will edit the plugins locally then until the plugins's authors put the modification. Thank you @julian for this quick fix. @a_5mith could you let us know when you have pushed it to npm or github please? 😉