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Improved test coverage and refactor of STIMPhysicalCircuit (#86)

See the opening comment of https://github.com/sandialabs/LoQS/pull/86 for a detailed description of changes. The TL;DR is as follows.

### 1. Refactored `STIMPhysicalCircuit.__init__`. 

The original monolithic constructor is split into module-level helpers (`_get_used_stim_indices`, `_reindex_stim_circuit`, `_separate_stimcircuit_instruction`, `_replace_instruction_targets`, `_as_stim_circuit`, `_check_label_count`) and a much shorter dispatch body. Behavior is preserved; the goal is to make the STIM/string/STIMPhysicalCircuit input branches reviewable independently.

### 2. New test files for `stimcircuit.py`, `stimdictmodel.py`, `pygstitools`, and `qsimtools`. 

The `STIMPhysicalCircuit` tests are organized into four `unittest.TestCase` classes by concern: init, mutators, queries, and helpers.

### 3. Minor cleanups. 

Fixed README typo, `pygstitools` typo, and a couple of type-annotations.

945 of 1144 branches covered (82.6%)

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5203 of 6454 relevant lines covered (80.62%)

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