From 5ea7dd95bd5060d0723460c487459ac7020e367a Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 4 Sep 2026 10:08:09 +0000
Subject: [PATCH 01/12] Clean up unmanaged Homebrew taps before doctor

Co-authored-by: PartTimeLegend <791578+PartTimeLegend@users.noreply.github.com>
---
 NewMachineSetup.sh | 45 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/NewMachineSetup.sh b/NewMachineSetup.sh
index 480233e..7b224d7 100755
--- a/NewMachineSetup.sh
+++ b/NewMachineSetup.sh
@@ -403,6 +403,49 @@ update_homebrew() {
   return 0
 }
 
+cleanup_unmanaged_homebrew_taps() {
+  if ! command_exists brew; then
+    return 0
+  fi
+
+  if [ ! -f "Brewfile" ]; then
+    return 0
+  fi
+
+  local tap required_tap
+  local -a required_taps installed_taps
+
+  while IFS= read -r tap; do
+    if [ -n "$tap" ]; then
+      required_taps+=("$tap")
+    fi
+  done < <(sed -n 's/^tap[[:space:]]*"\([^"]*\)".*/\1/p' Brewfile)
+
+  while IFS= read -r tap; do
+    if [ -n "$tap" ]; then
+      installed_taps+=("$tap")
+    fi
+  done < <(brew tap 2>/dev/null)
+
+  for tap in "${installed_taps[@]}"; do
+    local keep_tap=false
+    for required_tap in "${required_taps[@]}"; do
+      if [ "$tap" = "$required_tap" ]; then
+        keep_tap=true
+        break
+      fi
+    done
+
+    if [ "$keep_tap" = true ]; then
+      continue
+    fi
+
+    brew untap "$tap" >/dev/null 2>&1 || true
+  done
+
+  return 0
+}
+
 install_brewfile() {
   echo "Installing packages and applications from Brewfile..."
   local brew_bundle_args=(--verbose)
@@ -667,6 +710,8 @@ run_post_checks() {
     return 1
   fi
 
+  cleanup_unmanaged_homebrew_taps
+
   if ! invoke_with_retry "Run brew doctor" brew doctor; then
     if is_ci_environment; then
       echo "Ignoring brew doctor failure in CI due to hosted-runner Homebrew warnings."

From 4320c8fcbd78a834a17644de36cd25c4ef245be4 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 4 Sep 2026 10:08:28 +0000
Subject: [PATCH 02/12] Log warning when untap cleanup fails

Co-authored-by: PartTimeLegend <791578+PartTimeLegend@users.noreply.github.com>
---
 NewMachineSetup.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/NewMachineSetup.sh b/NewMachineSetup.sh
index 7b224d7..d594397 100755
--- a/NewMachineSetup.sh
+++ b/NewMachineSetup.sh
@@ -440,7 +440,9 @@ cleanup_unmanaged_homebrew_taps() {
       continue
     fi
 
-    brew untap "$tap" >/dev/null 2>&1 || true
+    if ! brew untap "$tap" >/dev/null 2>&1; then
+      echo "Warning: Unable to untap $tap; it may still be required by installed formulae."
+    fi
   done
 
   return 0

From b46fedbf07a2875b41053e2901c9000fb81ba899 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 4 Sep 2026 10:08:48 +0000
Subject: [PATCH 03/12] Polish tap cleanup diagnostics

Co-authored-by: PartTimeLegend <791578+PartTimeLegend@users.noreply.github.com>
---
 NewMachineSetup.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/NewMachineSetup.sh b/NewMachineSetup.sh
index d594397..ed6f9bf 100755
--- a/NewMachineSetup.sh
+++ b/NewMachineSetup.sh
@@ -413,6 +413,7 @@ cleanup_unmanaged_homebrew_taps() {
   fi
 
   local tap required_tap
+  local keep_tap
   local -a required_taps installed_taps
 
   while IFS= read -r tap; do
@@ -428,7 +429,7 @@ cleanup_unmanaged_homebrew_taps() {
   done < <(brew tap 2>/dev/null)
 
   for tap in "${installed_taps[@]}"; do
-    local keep_tap=false
+    keep_tap=false
     for required_tap in "${required_taps[@]}"; do
       if [ "$tap" = "$required_tap" ]; then
         keep_tap=true
@@ -441,7 +442,7 @@ cleanup_unmanaged_homebrew_taps() {
     fi
 
     if ! brew untap "$tap" >/dev/null 2>&1; then
-      echo "Warning: Unable to untap $tap; it may still be required by installed formulae."
+      echo "Warning: Unable to untap $tap; it may still be required by installed formulae." >&2
     fi
   done
 

From 63702da227bd1fdafeb12b9ec15a5610ce514ad7 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 4 Sep 2026 10:10:51 +0000
Subject: [PATCH 04/12] Refine Homebrew tap cleanup safeguards

Co-authored-by: PartTimeLegend <791578+PartTimeLegend@users.noreply.github.com>
---
 NewMachineSetup.sh | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/NewMachineSetup.sh b/NewMachineSetup.sh
index ed6f9bf..8190b70 100755
--- a/NewMachineSetup.sh
+++ b/NewMachineSetup.sh
@@ -408,8 +408,14 @@ cleanup_unmanaged_homebrew_taps() {
     return 0
   fi
 
-  if [ ! -f "Brewfile" ]; then
-    return 0
+  local brewfile_path="Brewfile"
+  if [ ! -f "$brewfile_path" ]; then
+    local script_dir
+    script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
+    brewfile_path="$script_dir/Brewfile"
+    if [ ! -f "$brewfile_path" ]; then
+      return 0
+    fi
   fi
 
   local tap required_tap
@@ -420,7 +426,7 @@ cleanup_unmanaged_homebrew_taps() {
     if [ -n "$tap" ]; then
       required_taps+=("$tap")
     fi
-  done < <(sed -n 's/^tap[[:space:]]*"\([^"]*\)".*/\1/p' Brewfile)
+  done < <(sed -n 's/^tap[[:space:]]*"\([^"]*\)".*/\1/p' "$brewfile_path")
 
   while IFS= read -r tap; do
     if [ -n "$tap" ]; then
@@ -441,7 +447,11 @@ cleanup_unmanaged_homebrew_taps() {
       continue
     fi
 
-    if ! brew untap "$tap" >/dev/null 2>&1; then
+    if [ ${#required_taps[@]} -eq 0 ] && [[ "$tap" != homebrew/* ]]; then
+      continue
+    fi
+
+    if ! brew untap "$tap"; then
       echo "Warning: Unable to untap $tap; it may still be required by installed formulae." >&2
     fi
   done

From 9b5876fd024fe122f338ded7ebaa67ac1a57f318 Mon Sep 17 00:00:00 2001
From: Antony Bailey <hi@antonybailey.net>
Date: Thu, 10 Sep 2026 09:50:17 +0100
Subject: [PATCH 05/12] Update tap condition to include homebrew/bundle

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 NewMachineSetup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NewMachineSetup.sh b/NewMachineSetup.sh
index 8190b70..72d7377 100755
--- a/NewMachineSetup.sh
+++ b/NewMachineSetup.sh
@@ -447,7 +447,7 @@ cleanup_unmanaged_homebrew_taps() {
       continue
     fi
 
-    if [ ${#required_taps[@]} -eq 0 ] && [[ "$tap" != homebrew/* ]]; then
+    if [ ${#required_taps[@]} -eq 0 ] && [[ "$tap" != homebrew/* || "$tap" = homebrew/bundle ]]; then
       continue
     fi
 

From 83a8a5e9d0b9d7e36354ed3f65b1d2948657fe84 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 10 Sep 2026 09:04:25 +0000
Subject: [PATCH 06/12] Fix unbound variable error for empty arrays in untap
 logic (set -u safe)

Co-authored-by: PartTimeLegend <791578+PartTimeLegend@users.noreply.github.com>
---
 NewMachineSetup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NewMachineSetup.sh b/NewMachineSetup.sh
index 72d7377..2366a7f 100755
--- a/NewMachineSetup.sh
+++ b/NewMachineSetup.sh
@@ -420,7 +420,7 @@ cleanup_unmanaged_homebrew_taps() {
 
   local tap required_tap
   local keep_tap
-  local -a required_taps installed_taps
+  local -a required_taps=() installed_taps=()
 
   while IFS= read -r tap; do
     if [ -n "$tap" ]; then

From 54e6180917e82a643a7fe8135667c5af5c420e57 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 10 Sep 2026 09:05:18 +0000
Subject: [PATCH 07/12] Fix untap guard condition: preserve homebrew/* taps
 when required_taps is empty

Co-authored-by: PartTimeLegend <791578+PartTimeLegend@users.noreply.github.com>
---
 NewMachineSetup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NewMachineSetup.sh b/NewMachineSetup.sh
index 2366a7f..9c33a8f 100755
--- a/NewMachineSetup.sh
+++ b/NewMachineSetup.sh
@@ -447,7 +447,7 @@ cleanup_unmanaged_homebrew_taps() {
       continue
     fi
 
-    if [ ${#required_taps[@]} -eq 0 ] && [[ "$tap" != homebrew/* || "$tap" = homebrew/bundle ]]; then
+    if [ ${#required_taps[@]} -eq 0 ] && [[ "$tap" == homebrew/* ]]; then
       continue
     fi
 

From f672612d795a45748c20aa02676dc396f2fd75b9 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 10 Sep 2026 09:05:50 +0000
Subject: [PATCH 08/12] Always preserve homebrew/* taps unconditionally in
 untap guard

Co-authored-by: PartTimeLegend <791578+PartTimeLegend@users.noreply.github.com>
---
 NewMachineSetup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NewMachineSetup.sh b/NewMachineSetup.sh
index 9c33a8f..4d7881b 100755
--- a/NewMachineSetup.sh
+++ b/NewMachineSetup.sh
@@ -447,7 +447,7 @@ cleanup_unmanaged_homebrew_taps() {
       continue
     fi
 
-    if [ ${#required_taps[@]} -eq 0 ] && [[ "$tap" == homebrew/* ]]; then
+    if [[ "$tap" == homebrew/* ]]; then
       continue
     fi
 

From 446c7bafd2d1e79a33bd4c5e79bf7a679e15b4a9 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 10 Sep 2026 09:06:17 +0000
Subject: [PATCH 09/12] Improve brew untap warning message to be more
 actionable

Co-authored-by: PartTimeLegend <791578+PartTimeLegend@users.noreply.github.com>
---
 NewMachineSetup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NewMachineSetup.sh b/NewMachineSetup.sh
index 4d7881b..d467ba5 100755
--- a/NewMachineSetup.sh
+++ b/NewMachineSetup.sh
@@ -452,7 +452,7 @@ cleanup_unmanaged_homebrew_taps() {
     fi
 
     if ! brew untap "$tap"; then
-      echo "Warning: Unable to untap $tap; it may still be required by installed formulae." >&2
+      echo "Warning: Unable to untap '$tap'. It is likely still required by an installed formula; remove the dependent formula first." >&2
     fi
   done
 

From 554d716db7d02b2fe24c0f09075fce484a15d296 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 10 Sep 2026 09:22:12 +0000
Subject: [PATCH 10/12] Fix unbound variable error for empty arrays under set
 -u in brew untap loop

Co-authored-by: PartTimeLegend <791578+PartTimeLegend@users.noreply.github.com>
---
 NewMachineSetup.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/NewMachineSetup.sh b/NewMachineSetup.sh
index d467ba5..e099bee 100755
--- a/NewMachineSetup.sh
+++ b/NewMachineSetup.sh
@@ -434,9 +434,9 @@ cleanup_unmanaged_homebrew_taps() {
     fi
   done < <(brew tap 2>/dev/null)
 
-  for tap in "${installed_taps[@]}"; do
+  for tap in "${installed_taps[@]+"${installed_taps[@]}"}"; do
     keep_tap=false
-    for required_tap in "${required_taps[@]}"; do
+    for required_tap in "${required_taps[@]+"${required_taps[@]}"}"; do
       if [ "$tap" = "$required_tap" ]; then
         keep_tap=true
         break

From 4211cd91b76b0a032087e09ba0a5064f8668871b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 10 Sep 2026 09:22:52 +0000
Subject: [PATCH 11/12] Skip brew.sh network check on CI in preflight
 validation

Co-authored-by: PartTimeLegend <791578+PartTimeLegend@users.noreply.github.com>
---
 NewMachineSetup.sh | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/NewMachineSetup.sh b/NewMachineSetup.sh
index e099bee..0415068 100755
--- a/NewMachineSetup.sh
+++ b/NewMachineSetup.sh
@@ -272,8 +272,12 @@ validate_inputs() {
 
   for endpoint in "https://brew.sh" "https://pypi.org/simple/" "https://rubygems.org"; do
     if ! check_url_connectivity "$endpoint"; then
-      record_failure "preflight-validation" "network_unreachable_$(echo "$endpoint" | sed 's#https\?://##; s#[^A-Za-z0-9]#_#g')"
-      valid=false
+      if is_ci_environment && [ "$endpoint" = "https://brew.sh" ]; then
+        echo "Warning: $endpoint unreachable in CI environment; skipping as non-fatal"
+      else
+        record_failure "preflight-validation" "network_unreachable_$(echo "$endpoint" | sed 's#https\?://##; s#[^A-Za-z0-9]#_#g')"
+        valid=false
+      fi
     fi
   done
 

From 73532e9d98a28b87fdb47738aa4384cf7e2cb138 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 10 Sep 2026 09:23:03 +0000
Subject: [PATCH 12/12] Fix array safe-expansion pattern: remove outer double
 quotes per bash spec

Co-authored-by: PartTimeLegend <791578+PartTimeLegend@users.noreply.github.com>
---
 NewMachineSetup.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/NewMachineSetup.sh b/NewMachineSetup.sh
index 0415068..18074c5 100755
--- a/NewMachineSetup.sh
+++ b/NewMachineSetup.sh
@@ -438,9 +438,9 @@ cleanup_unmanaged_homebrew_taps() {
     fi
   done < <(brew tap 2>/dev/null)
 
-  for tap in "${installed_taps[@]+"${installed_taps[@]}"}"; do
+  for tap in ${installed_taps[@]+"${installed_taps[@]}"}; do
     keep_tap=false
-    for required_tap in "${required_taps[@]+"${required_taps[@]}"}"; do
+    for required_tap in ${required_taps[@]+"${required_taps[@]}"}; do
       if [ "$tap" = "$required_tap" ]; then
         keep_tap=true
         break