docs: clarify PR comment workflow sequence

Make it explicit that PR comment management is a two-step process:
1. Get comments first (to retrieve thread IDs)
2. Use those thread IDs to reply/resolve

Changes:
- Add 'Workflow Overview' section in tools.md
- Add step numbers and explanatory notes
- Clarify that thread-id comes from step 1 output
- Add workflow summary to quick-reference.md

This prevents confusion about where thread IDs come from and makes
the command sequence clear.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: codepuncher

shell/copilot-instructions/quick-reference.md

@@ -112,9 +112,11 @@ wp @production cache flush         # Write operation: be careful
 
 ## PR Comment Management
 
+**Workflow:** Get comments first (to find thread IDs), then reply/resolve using those IDs.
+
 ### Get Comments
 ```bash
-# All comments in pretty format
+# Step 1: Get all comments (includes thread IDs in output)
 ~/Code/misc/itineris-bin/gh-pr-get-comments <pr-number>
 
 # Filter by author
@@ -130,9 +132,9 @@ wp @production cache flush         # Write operation: be careful
 
 ### Reply to Comments
 ```bash
-# Reply to thread
+# Step 2: Reply using thread-id from step 1
 ~/Code/misc/itineris-bin/gh-pr-reply-to-thread <pr-number> \
-  --thread-id='PRRT_kwDOABCDEF' \
+  --thread-id='PRRT_xxx' \
   --message='Fixed in commit abc1234'
 
 # Reply and resolve

shell/copilot-instructions/tools.md

@@ -4,12 +4,17 @@ Scripts, utilities, and tools available for Itineris development workflows.
 
 ## GitHub PR Comment Management
 
-### Get PR Comments
+### Workflow Overview
 
-Use `gh-pr-get-comments` script to retrieve all comments on a PR:
+1. **First:** Get PR comments to see thread IDs
+2. **Then:** Reply/resolve specific threads using the thread IDs from step 1
+
+### Step 1: Get PR Comments
+
+Use `gh-pr-get-comments` to retrieve all comments and their thread IDs:
 
 ```bash
-# Get all comments in pretty format
+# Get all comments in pretty format (includes thread IDs)
 ~/Code/misc/itineris-bin/gh-pr-get-comments <pr-number>
 
 # Filter by author (e.g., Copilot bot)
@@ -22,9 +27,11 @@ Use `gh-pr-get-comments` script to retrieve all comments on a PR:
 ~/Code/misc/itineris-bin/gh-pr-get-comments <pr-number> --format=json
 ```
 
-### Reply to PR Comments
+**Note:** The output includes `thread-id` values (e.g., `PRRT_kwDOABCDEF`) which you need for the next step.
+
+### Step 2: Reply to PR Comments
 
-Use `gh-pr-reply-to-thread` script to reply and resolve review threads:
+Use `gh-pr-reply-to-thread` with the thread-id from step 1:
 
 ```bash
 # Reply to a review thread (use thread-id from gh-pr-get-comments output)

shell/functions

@@ -203,6 +203,8 @@ install_wsl_packages() {
   install_git_delta
   # ensure fd is available
   ln -sf "$(which fdfind)" ~/.local/bin/fd
+  # ensure bat is available
+  ln -sf "$(which batcat)" ~/.local/bin/bat
 }
 
 setup_arch_services() {

terminals/alacritty.toml

@@ -50,7 +50,7 @@ decorations = "None"
 decorations_theme_variant = "Dark"
 dynamic_padding = true
 dynamic_title = true
-opacity = 0.75
+opacity = 1
 startup_mode = "Maximized"
 
 [window.padding]