Remove deprecated formats, update reader and writer backends #1646

Job	Run time
Bleeding Edge mosdef Tests for mBuild	3m 21s
mBuild Tests (macOS-latest, 3.9)	9m 8s
mBuild Tests (macOS-latest, 3.10)	7m 28s
mBuild Tests (macOS-latest, 3.11)	7m 6s
mBuild Tests (macOS-latest, 3.12)	9m 12s
mBuild Tests (macOS-13, 3.9)	17m 4s
mBuild Tests (macOS-13, 3.10)	16m 37s
mBuild Tests (macOS-13, 3.11)	15m 34s
mBuild Tests (macOS-13, 3.12)	22m 47s
mBuild Tests (ubuntu-latest, 3.9)	9m 34s
mBuild Tests (ubuntu-latest, 3.10)	8m 31s
mBuild Tests (ubuntu-latest, 3.11)	7m 37s
mBuild Tests (ubuntu-latest, 3.12)	10m 5s
mBuild Tests (windows-latest, 3.12)	15m 49s
Build Docker Image	0s
	2h 39m 53s

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