Qiskit / qiskit-ibm-runtime / 27833831789

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Reorganize executor-estimator folder consistently (#2936)

### Summary
This PR does not add or remove code, just moves it around for better
organization and consistency.
In more details:
- It moves functions used by every `prepare` (for example,
`box_circuit`) out of `prepare.py` and into `utils.py`.
- It renames files consistently (for example, `pec_utils.py` ->
`prepare_pec.py`)
- It updates test files accordingly

AI disclaimer:
- [x] I didn't use LLM tooling, or only used it privately.

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