fix: improve upgrade command based on real usage feedback

- Add check for files that exist in upstream before updating
- Add version comparison to avoid unnecessary upgrades
- Add batch update examples for similar files
- Better handling of missing upstream files (like deprecated agents)
- Include instructions for finding NEW files in upstream
- Clearer error messages when files don't exist

.claude/commands/upgrade.md

@@ -29,6 +29,16 @@ capabilities.
 ### 1. **Version Check & Setup**
 
 - Get current version from package.json
+- Check if already on latest version:
+  ```bash
+  CURRENT=$(grep '"version"' package.json | sed 's/.*: "\(.*\)".*/\1/')
+  LATEST=$(curl -s https://raw.githubusercontent.com/heyitsnoah/claudesidian/main/package.json | grep '"version"' | sed 's/.*: "\(.*\)".*/\1/')
+
+  if [ "$CURRENT" = "$LATEST" ]; then
+    echo "✅ You're already on the latest version ($CURRENT)"
+    exit 0
+  fi
+  ```
 - Create timestamped backup in `.backup/upgrade-YYYY-MM-DD-HHMMSS/`:
   ```bash
   # Create backup directory
@@ -55,10 +65,17 @@ capabilities.
 
 - Compare system files between current directory and .tmp/claudesidian-upgrade/:
   ```bash
-  # Find all system files that differ
+  # Find all system files that differ AND new files in upstream
+  # First, find files that exist in both but differ
   diff -qr . .tmp/claudesidian-upgrade/ --include="*.md" --include="*.sh" --include="*.json" |
   grep -E '(\.claude/|\.scripts/|package\.json|CHANGELOG\.md|README\.md)' |
   grep -v '(00_|01_|02_|03_|04_|05_|06_|\.obsidian|CLAUDE\.md)'
+
+  # Also find NEW files in upstream (like new commands)
+  find .tmp/claudesidian-upgrade/.claude/commands -name "*.md" | while read f; do
+    local_file=${f#.tmp/claudesidian-upgrade/}
+    [ ! -f "$local_file" ] && echo "NEW: $local_file"
+  done
   ```
 - Create checklist of files that need review
 - Explicitly EXCLUDE:
@@ -130,10 +147,12 @@ For EACH file in the checklist:
 4.  Apply the chosen strategy:
     - **For option 1 (Apply update/Take upstream)**:
       ```bash
-      # IMPORTANT: Use cat with redirection to avoid ALL prompts
-      # Do NOT use cp or cp -f as they may still prompt on some systems
-      cat .tmp/claudesidian-upgrade/path/to/file > path/to/file && echo "✅ Updated"
-      # Alternative if needed: rm -f path/to/file && cat .tmp/claudesidian-upgrade/path/to/file > path/to/file
+      # IMPORTANT: Check if file exists first, then use cat with redirection
+      if [ -f ".tmp/claudesidian-upgrade/path/to/file" ]; then
+        cat .tmp/claudesidian-upgrade/path/to/file > path/to/file && echo "✅ Updated"
+      else
+        echo "⚠️ File not found in upstream - keeping local version"
+      fi
       ```
     - **For option 2 (Keep your version)**:
       ```bash
@@ -155,6 +174,28 @@ For EACH file in the checklist:
 - **Needs review**: `package.json` (preserve user's custom scripts)
 - **Never touch**: User content folders, CLAUDE.md, API configs
 
+#### Batch Updates for Similar Files
+For commands that have only formatting changes, you can batch update:
+```bash
+# Batch update multiple command files with same type of changes
+for file in thinking-partner.md daily-review.md inbox-processor.md; do
+  if [ -f ".tmp/claudesidian-upgrade/.claude/commands/$file" ]; then
+    cat ".tmp/claudesidian-upgrade/.claude/commands/$file" > ".claude/commands/$file"
+    echo "✅ Updated $file"
+  fi
+done
+```
+
+#### Handling Missing Upstream Files
+Some files may exist locally but not in upstream (like deprecated agents):
+```bash
+# Check if file exists in upstream before trying to update
+if [ ! -f ".tmp/claudesidian-upgrade/$filepath" ]; then
+  echo "⚠️ $filepath not in upstream - keeping local version"
+  # Mark as skipped in checklist: [-]
+fi
+```
+
 ### 5. **Progress Tracking**
 
 - Use TodoWrite tool to track progress alongside the checklist