Misc cleanup

[5h4ng]

Apply selected quick wins to improve pipeline stability and code quality.

• Fix config handling:
  • avoid splitting a single inputFile string into characters
  • standardize numProcess to numProcesses in config/CLI/tests
• Improve pipeline experiment cleanup by initializing results/models before try/finally.
• Reduce plotting memory retention by adding plt.close("all") after save/show.
• Clean up minor technical debt:
  • remove unused CLI helper
  • fix PWM method typo
  • remove redundant return selection in mhcflurry
  • move re import to module top
  • remove non-English inline comment

[5h4ng]

@codex review

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. Breezy!

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