Refactor `from_spec_modules` in `APRProof` #6069

Job	Run time
Java: Linting	1m 27s
Pyk: Code Quality & Unit Tests (3.10)	1m 28s
Pyk: Code Quality & Unit Tests (3.11)	1m 15s
Pyk: Code Quality & Unit Tests (3.12)	1m 19s
Code Quality Checks	1s
Pyk: Nix Build (ubuntu-latest)	38s
K: Source Build & Test	16m 59s
Pyk: Nix Build (macos-14)	1m 17s
K: Ubuntu Jammy Frontend Package	20m 49s
K: Nix Build & Test (self-hosted, linux, normal)	5m 28s
K: Ubuntu Jammy Package	20m 0s
K: Nix Build & Test (MacM1, self-macos-12)	23m 36s
Pyk: Integration Tests	19m 7s
Pyk: Documentation	5m 4s
K: Profiling	11m 37s
Pyk: Profiling	4m 11s
Pyk: Regression Tests	17m 28s
	2h 31m 44s

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