refactor: Apply codebase audit improvements

CLAUDE.md

@@ -84,6 +84,7 @@ The `.zshrc` file sources other configuration files in this order:
 - Incremental, case-smart search with highlighting
 - No swap/backup files
 - Line numbers and always-visible status line
+- Uses Catppuccin mocha (dark) theme only; light mode switching not implemented
 
 **Dark Mode Theme Switching** (home/.bin/toggle-btop-theme)
 - Automatically switches btop theme based on macOS appearance

LaunchAgents/com.user.dark-notify.plist

@@ -8,7 +8,7 @@
     <true/>
     <key>ProgramArguments</key>
     <array>
-        <string>/opt/homebrew/bin/dark-notify</string>
+        <string>__HOMEBREW_PREFIX__/bin/dark-notify</string>
         <string>-c</string>
         <string>__HOME__/.bin/toggle-btop-theme</string>
     </array>

bootstrap.sh

@@ -1,4 +1,5 @@
 #!/usr/bin/env bash
+set -euo pipefail
 
 # ==============================================================================
 # Bootstrap Script - Install Dotfiles
@@ -96,18 +97,28 @@ install_launch_agents() {
 	# Install dark-notify LaunchAgent (only if dark-notify is installed)
 	if command -v dark-notify >/dev/null 2>&1; then
 		local plist="com.user.dark-notify.plist"
+		local homebrew_prefix
+		if command -v brew >/dev/null 2>&1 && homebrew_prefix="$(brew --prefix 2>/dev/null)"; then
+			: # homebrew_prefix set by condition
+		elif [[ "$(uname -m)" == "arm64" ]]; then
+			homebrew_prefix="/opt/homebrew"
+		else
+			homebrew_prefix="/usr/local"
+		fi
 		local new_plist_content
-		new_plist_content=$(sed "s|__HOME__|$HOME|g" "LaunchAgents/$plist")
+		new_plist_content=$(sed -e "s|__HOME__|$HOME|g" -e "s|__HOMEBREW_PREFIX__|$homebrew_prefix|g" "LaunchAgents/$plist")
 		local dest_plist="$launch_agents_dir/$plist"
 
 		# Only update and reload if plist content changed
 		local tmp_plist
 		tmp_plist=$(mktemp)
+		trap 'rm -f "$tmp_plist"' EXIT
 		echo "$new_plist_content" > "$tmp_plist"
 
 		if [[ ! -f "$dest_plist" ]] || ! cmp -s "$tmp_plist" "$dest_plist"; then
 			echo "Installing LaunchAgent: $plist"
 			mv "$tmp_plist" "$dest_plist"
+			trap - EXIT
 
 			# Reload the agent
 			launchctl bootout "gui/$(id -u)/com.user.dark-notify" 2>/dev/null || true
@@ -117,6 +128,7 @@ install_launch_agents() {
 			"$HOME/.bin/toggle-btop-theme"
 		else
 			rm -f "$tmp_plist"
+			trap - EXIT
 		fi
 	else
 		echo "Skipping dark-notify LaunchAgent (dark-notify not installed)"
@@ -205,7 +217,7 @@ sync_dotfiles() {
 	install_launch_agents
 
 	# Reload zsh configuration
-	if [[ -n "$ZSH_VERSION" ]]; then
+	if [[ -n "${ZSH_VERSION:-}" ]]; then
 		source ~/.zshrc 2>/dev/null || echo "Restart your terminal or run: source ~/.zshrc"
 	fi
 }

home/.claude/commands/im-lost.md

@@ -20,13 +20,15 @@ git status --short
 # Recent commits on this branch (vs main)
 git log main..HEAD --oneline 2>/dev/null || git log -3 --oneline
 
-# Check for open PR on current branch
-gh pr view --json number,title,state,statusCheckRollup,reviewDecision,comments 2>/dev/null
+# Check for open PR on current branch (includes linked issue)
+gh pr view --json number,title,state,statusCheckRollup,reviewDecision,comments,body 2>/dev/null
 
 # Check active todos
 # (Read from conversation context)
 ```
 
+Parse the PR body for issue references (e.g., "Fixes #123", "Closes #45", or issue URLs). If found, fetch the linked issue for additional context.
+
 ### 2. Determine Workflow Position
 
 Based on gathered state, identify the current step:
@@ -51,6 +53,7 @@ Present in this format:
 **Branch:** [branch-name]
 **Status:** [uncommitted changes summary or "clean"]
 **PR:** [#N - title (CI status, N comments)] or "none"
+**Issue:** [#N - title] or "none"
 
 ### Workflow Position
 
@@ -67,11 +70,11 @@ Present in this format:
 
 ### Context
 
-[2-3 sentences summarizing recent work based on branch name, commits, and PR description]
+[2-3 sentences summarizing recent work based on branch name, commits, PR description, and linked issue if any. Reference the issue number when describing what problem is being solved.]
 
 ### Suggested Next Action
 
-[One concrete action to take, with the command to run if applicable]
+[One concrete action to take, with the command to run if applicable. If working on an issue, frame the action in terms of completing that issue.]
 ```
 
 ### 4. Guidelines
@@ -81,3 +84,4 @@ Present in this format:
 - If on main with no changes, suggest running `/status-report` to find work
 - If stuck between steps, pick the earlier one
 - Reference active todos if any exist in the conversation
+- If working on an issue, always mention the issue number in Context and Suggested Next Action

home/.claude/commands/pr-feedback.md

@@ -62,11 +62,17 @@ Before presenting interactive questions, output ALL feedback items ordered by se
 > Fix JSON interface to handle missing fields
 **Opinion**: Agree - breaking change needs fix
 
-#### #2. [Suggestion] `utils.ts:89` (Local)
+#### #2. [Important] `bootstrap.sh:42` (Local)
+> Validate input before processing
+**Opinion**: Agree - defensive programming
+
+#### #3. [Suggestion] `utils.ts:89` (Remote)
 > Add error handling for missing PR
 **Opinion**: Disagree - edge case, unlikely to occur
 ```
 
+**Important**: Items MUST be numbered in severity order - all Critical items first, then Important, then Suggestion. The `#N` numbering follows this order.
+
 **Source indicators**: `(Local)` = from pr-review-toolkit, `(Remote)` = from external reviewers
 
 Numbers match the `#N` headers in the AskUserQuestion step.

home/.exports

@@ -2,6 +2,9 @@
 # Environment Variables
 # ==============================================================================
 
+# Variables expected in ~/.extra (not tracked):
+#   GITHUB_TOKEN - Required for Claude Code GitHub MCP server
+
 # PATH configuration
 if [ -d "$HOME/.local/bin" ]; then
     export PATH="$HOME/.local/bin:$PATH"

home/.zshrc

@@ -18,6 +18,7 @@ zstyle ':completion:*' use-cache on
 zstyle ':completion:*' cache-path ~/.zsh/cache
 
 # History
+HISTFILE=~/.zsh_history
 HISTSIZE=32768
 SAVEHIST=32768
 setopt APPEND_HISTORY

preferences/iTerm Profile.json

@@ -649,4 +649,4 @@
     "Alpha Component" : 1,
     "Green Component" : 0.37254901960784315
   }
-}
+}

uninstall.sh

@@ -1,4 +1,5 @@
 #!/usr/bin/env bash
+set -euo pipefail
 
 # ==============================================================================
 # Uninstall Script - Remove Dotfiles