Improve project setup CLI readability

[michaelhallquist]

Summary

• standardize setup prompts with terminal-width section rules, wrapped paragraphs, and consistently indented lists
• extend shared CLI helpers for instructions, section headings, and numbered values without changing the TTY-safe input reader
• preserve argument-driven headless setup for the non-interactive BrainGnomes CLI route
• document the prompt heading option and add coverage for formatting, TTY input, and headless initialization

Testing

• devtools::document()
• devtools::test() (2,143 passed, 1 existing opt-in Slurm integration skip)
• direct TTY-connected Rscript prompt smoke test
• installed-package BrainGnomes setup_project --non-interactive smoke test plus JSON configuration validation
• devtools::check() completed installation, tests, examples, documentation, and vignette rebuilds with 0 errors; this environment reported the expected missing-qpdf warning and notes for clock verification and the existing -Wconversion compilation flag