Remove deprecated formats, update reader and writer backends #1594

Job	Run time
Bleeding Edge mosdef Tests for mBuild	3m 8s
mBuild Tests (macOS-latest, 3.9)	9m 33s
mBuild Tests (macOS-latest, 3.10)	8m 18s
mBuild Tests (macOS-latest, 3.11)	8m 1s
mBuild Tests (macOS-latest, 3.12)	11m 36s
mBuild Tests (macOS-13, 3.9)	18m 7s
mBuild Tests (macOS-13, 3.10)	14m 45s
mBuild Tests (macOS-13, 3.11)	15m 48s
mBuild Tests (macOS-13, 3.12)	20m 3s
mBuild Tests (ubuntu-latest, 3.9)	9m 47s
mBuild Tests (ubuntu-latest, 3.10)	8m 32s
mBuild Tests (ubuntu-latest, 3.11)	7m 54s
mBuild Tests (ubuntu-latest, 3.12)	9m 57s
mBuild Tests (windows-latest, 3.12)	16m 53s
Build Docker Image	0s
	2h 42m 22s

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