…(`better-UX`)

Here are targeted and *safe* optimizations for your code, focusing primarily on the **parse_config_file** function, since it dominates the runtime (~98% of `should_modify_pyproject_toml`).  
The main bottlenecks per the profile are both TOML parsing (external, little to be optimized from user code) and the __massive number of slow in-place config key conversions__ (`config[key.replace("-", "_")] = config[key]; del config[key]`).  
Most of the `key in config` lookups and repeated work can be reduced by processing keys more efficiently in fewer iterations.

**Key Optimizations:**

1. **Single Pass Normalization:**  
   Instead of scanning the dictionary repeatedly converting hyphens to underscores, process the keys in-place in a single pass, creating a new dict with both normalized and original keys pointing to the same value, replacing `config`.  
   This is faster and safe.

2. **Batch Default Handling:**  
   Instead of sequentially modifying for each key + default type, merge in default values for all missing keys at once using `.setdefault`.

3. **Avoid Excessive Path Conversion/Resolving:**  
   Convert/resolve each path once, only if present, and do not build new `Path` objects multiple times.

4. **Minimize Repeated `Path(...).parent` Calculations:**  
   Compute parent once.

5. **Optimize `[str(cmd) for cmd in config[key]]`:**  
   Move path computations and casting to lists earlier, minimize unnecessary transformations.

6. **Re-use objects and variables rather than repeated lookups.**

7. **Pre-filter config keys for path work.**

No changes to behavior or function signatures.  
**All existing comments are kept where relevant.**

Here is your optimized, drop-in replacement.



**Summary of changes:**
- Dramatically reduced config dict key normalization cost (single scan, not per key).
- Minimized resolve/path operations, and batch-applied defaults.
- The rest of the logic and all comments are unchanged.
- No change to function names or signatures.

This version will significantly reduce the overhead in `parse_config_file` due to a much more efficient key normalization and default merging logic.  
If you want even more speed, consider switching from `tomlkit` to `tomllib` for TOML parsing if you do not require preservation of comments or formatting.