Fixes manual runtimes without modifying the construction of every object

Loads configuration before map creation instead.

This reverts commit 37b14bae39ae46b2397c0cbabce806790a03bd5c.
Fixes a typo in the Hydroponics reagents
Fixes colour mix up

Somehow phoron got the colour meant for inaprovaline.
Removes merc. RIG, fixes map bugs.
Removed mercenary RIG from the nukeop station. Swapped floor tile in one of the pens on wizard station for the correct one. Fixed nukeop shuttle transit 'space' turfs that had incorrect texture. Made nukeop transit 'thrower' object line symmetrical.
Fixes handle_organs() being called twice in Life()
Fixes #6240
Fixes #7406
Merge pull request #7455 from SparklySheep/patch-10

Fixes a typo in the Hydroponics reagents
Merge pull request #7447 from mwerezak/manual-runtime

Alternative fix for manual runtimes
Merge pull request #7458 from mwerezak/chem-colours

Fixes colour mix up
Merge pull request #7462 from mwerezak/life

Human Life() fixes
Removes ninja mask, fixes ninja internals
Merge pull request #7459 from Amunak/level2-fixes

Removes mercenary RIG, fixes Z-level 2 map bugs
Merge pull request #7460 from mwerezak/stance

 Fixes #7406
Reverts admin log colour.
Makes asay purple again.
Makes admin log messages bold again.
Makes 'other' PM colour way darker.
Merge pull request #7468 from Amunak/patch-1

Reverts admin log format, fixes colours
Fixes broken piping

Replaces round-start broken piping with endcaps, lines up atmos UPAs.
Fixes intercooler piping preventing the h/e from doing much cooling.