[MAP][DO NOT MERGE!] Overhaul of Boxstation's atmo piping

I am currently effecting a overhaul of Box's atmo piping layout, the current piping we have is very inconsistent and messy with no real sense of coherence or logical placement at time.

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The plan is simple, there will be a "primary pipe line" that runs through maintenance, from here a single pipe connection will branch off into every individual department. The primary pipe line will for the most part stay in maintenance, only going across hallways to connect between maint points.

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I'm opening this PR primarily to garner feedback, as well as get myself doing the changes.

Checklist of departments to repipe.

* Medical - DONE
* Science - DONE
* Atmospherics 
* Civilian Sector (Bar, Chapel, Kitchen, etc)
* Security
* Cargo
* Command
* Non-Department Sectors (Garden, arrivals, anywhere else)
* AI Satellite - DONE