After some digging around, I found a reddit post about starbound nightly. In it, there was this command:
/giveessentialitem beamaxe beamaxe
This is what unlocks your matter manipulator in its slot under your hotbar.

I also found these commands from the same reddit post, which will unlock the wiring and painting tools, or you could just collect enough manipulator modules to get the genuinely, but here they are:
/giveessentialitem wiretool wiretool
/giveessentialitem painttool painttool

I found the name of the item slot for the inspector tool by looking through the commands list after the latest update, but there doesn't seem to be an item for it, but here it is:
inspectiontool

To all of you that may want to read the reddit post I mentioned, and for the sake of not being an ♥♥♥♥♥♥♥, this is where I found the post:

https://www.reddit.com/r/starbound/comments/4jnhjw/nightly_faq_so_you_want_to_play_nightly/


Have fun!