Remove deprecated formats, update reader and writer backends #1647

Job	Run time
Bleeding Edge mosdef Tests for mBuild	3m 10s
mBuild Tests (macOS-latest, 3.9)	8m 12s
mBuild Tests (macOS-latest, 3.10)	8m 6s
mBuild Tests (macOS-latest, 3.11)	7m 33s
mBuild Tests (macOS-latest, 3.12)	8m 56s
mBuild Tests (macOS-13, 3.9)	23m 17s
mBuild Tests (macOS-13, 3.10)	17m 42s
mBuild Tests (macOS-13, 3.11)	20m 14s
mBuild Tests (macOS-13, 3.12)	43m 45s
mBuild Tests (ubuntu-latest, 3.9)	9m 50s
mBuild Tests (ubuntu-latest, 3.10)	8m 31s
mBuild Tests (ubuntu-latest, 3.11)	7m 34s
mBuild Tests (ubuntu-latest, 3.12)	9m 51s
mBuild Tests (windows-latest, 3.12)	17m 59s
Build Docker Image	0s
	3h 14m 40s

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