Restructure of tests

Some tests are located in the `src/tests` directory. A lot of these unit tests should be instead be in a `tests` submodule in the relevant module to uphold the Rust standard (https://doc.rust-lang.org/book/ch11-03-test-organization.html). For example, a lot of the clock reduction tests should probably be moved to `src/System/extract_system_rep.rs` and `src/TransitionSystems/transition_system.rs`.

Read the Rust test-organization guidance linked in the issue, then inspect tests under `src/tests` and the relevant modules. The issue specifically identifies `src/System/extract_system_rep.rs` and `src/TransitionSystems/transition_system.rs` as destinations for clock reduction tests. Done means the applicable unit tests are organized in module-local `tests` submodules and the existing test suite still passes.

Written by the indexing model from the issue text.