Untap unmanaged Homebrew taps before brew doctor in setup flow

[Copilot]

Homebrew health checks were noisy/failing due to unnecessary local taps (notably homebrew/core) being present during validation. This change adds deterministic tap hygiene before brew doctor so only explicitly declared taps are retained.

• Tap hygiene before post-checks

  • Added cleanup_unmanaged_homebrew_taps() and invoked it in run_post_checks() prior to brew doctor.
  • Enumerates installed taps and untaps any not declared via tap "..." entries in Brewfile.

• Brewfile resolution robustness

  • Resolves Brewfile from CWD first, then falls back to script directory, so cleanup runs correctly when invoked outside repo root.

• Failure visibility

  • If brew untap fails (e.g., still referenced by installed formulae), the script emits a warning to stderr instead of failing the run.

cleanup_unmanaged_homebrew_taps
invoke_with_retry "Run brew doctor" brew doctor

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[Copilot]

🟡 Changes recommended

Current empty-Brewfile behavior can untap essential homebrew/* taps (e.g., homebrew/bundle), which may have unintended post-setup side effects.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Pull request overview

This PR adds a Homebrew tap “hygiene” step to the Bash setup flow so brew doctor runs with a deterministic (and less noisy) set of taps, based on what’s declared in the repository Brewfile.

Changes:

• Added cleanup_unmanaged_homebrew_taps() to enumerate current taps and untap anything not declared in Brewfile.
• Updated Brewfile resolution logic to use CWD first, then fall back to the script directory.
• Invoked tap cleanup in run_post_checks() immediately before brew doctor, treating untap failures as warnings.

File summaries

File	Description
NewMachineSetup.sh	Adds tap-cleanup helper and runs it before brew doctor during post-checks.

Review details

• Files reviewed: 1/1 changed files
• Comments generated: 1
• Review effort level: Lite

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