scripts: avoid yq accessing files directly

scripts/install_collections.sh

@@ -45,11 +45,10 @@ while read -r manifest_path; do
         # Use yq to update items.src
         # 1. Prepend relative dir to everything
         # 2. Fix absolute paths to remain absolute
-        cp "$manifest_path" "${manifest_path}.tmp"
-        yq -i e "
+        cat "$manifest_path" | yq e "
             .[] .items[] .src |= \"$rel_dir\" + . |
             .[] .items[] .src |= sub(\"^$rel_dir/\", \"\")
-        " "${manifest_path}.tmp"
+        " | tee "${manifest_path}.tmp" > /dev/null
         cat "${manifest_path}.tmp" >> "$MERGED_MANIFEST"
         rm "${manifest_path}.tmp"
     fi
@@ -63,7 +62,7 @@ if [ ! -s "$MERGED_MANIFEST" ]; then
 fi
 
 # 3. Parse Collections from Config
-COLLECTIONS_LIST=$(yq '.copilot.collections[]' "$CONFIG_FILE" | tr '\n' ' ')
+COLLECTIONS_LIST=$(cat "$CONFIG_FILE" | yq '.copilot.collections[]' | tr '\n' ' ')
 
 if [ -z "$COLLECTIONS_LIST" ]; then
     echo "⚠️  No collections found in config file."
@@ -76,33 +75,33 @@ process_collection() {
     local col_name=$1
     echo "   📦 Processing Collection: $col_name"
 
-    if ! yq -e ".${col_name}" "$MERGED_MANIFEST" > /dev/null; then
+    if ! cat "$MERGED_MANIFEST" | yq -e ".${col_name}" > /dev/null; then
         echo "   ❌ Error: Collection '$col_name' not found in any manifest."
         exit 1
     fi
 
     # Handle Includes (Recursion)
     local includes
-    includes=$(yq ".${col_name}.includes[]" "$MERGED_MANIFEST" 2>/dev/null || true)
+    includes=$(cat "$MERGED_MANIFEST" | yq ".${col_name}.includes[]" 2>/dev/null || true)
     for included_col in $includes; do
         process_collection "$included_col"
     done
 
     # Handle Items
     local count
-    count=$(yq ".${col_name}.items | length" "$MERGED_MANIFEST")
+    count=$(cat "$MERGED_MANIFEST" | yq ".${col_name}.items | length")
 
     if [ "$count" -gt 0 ]; then
         for ((i=0; i<count; i++)); do
             local src dest
-            src=$(yq ".${col_name}.items[$i].src" "$MERGED_MANIFEST")
-            dest=$(yq ".${col_name}.items[$i].dest" "$MERGED_MANIFEST")
-            
+            src=$(cat "$MERGED_MANIFEST" | yq ".${col_name}.items[$i].src")
+            dest=$(cat "$MERGED_MANIFEST" | yq ".${col_name}.items[$i].dest")
+
             # Resolve full path for source
             local full_src="$TOOLKIT_DIR/$src"
 
             echo "      - Installing $src -> $dest"
-            
+
             if [ -d "$full_src" ]; then
                 # Folder Copy
                 mkdir -p "$dest"

scripts/local_sync.sh

@@ -56,7 +56,7 @@ fi
 
 echo -e "${BLUE}📄 Using config:${NC} $CONFIG_FILE"
 
-VERSION=$(yq '.copilot.version' "$CONFIG_FILE")
+VERSION=$(cat "$CONFIG_FILE" | yq '.copilot.version')
 if [ "$VERSION" == "null" ] || [ -z "$VERSION" ]; then
      echo -e "${RED}❌ Error: Could not read '.copilot.version' from $CONFIG_FILE${NC}"
      exit 1

scripts/validate_collections.sh

@@ -32,7 +32,7 @@ FAILED=0
 while read -r manifest; do
     # Get keys (collection names)
     # We use -r to get raw output (no quotes)
-    keys=$(yq e 'keys | .[]' "$manifest" 2>/dev/null || true)
+    keys=$(cat "$manifest" | yq e 'keys | .[]' 2>/dev/null || true)
 
     for key in $keys; do
         if [[ -n "${ALL_COLLECTIONS[$key]}" ]]; then
@@ -56,11 +56,11 @@ echo "   - Checking referential integrity..."
 
 while read -r manifest; do
     manifest_dir=$(dirname "$manifest")
-    keys=$(yq e 'keys | .[]' "$manifest" 2>/dev/null || true)
+    keys=$(cat "$manifest" | yq e 'keys | .[]' 2>/dev/null || true)
 
     for col in $keys; do
         # Check Includes
-        includes=$(yq e ".[\"$col\"].includes[]" "$manifest" 2>/dev/null || true)
+        includes=$(cat "$manifest" | yq e ".[\"$col\"].includes[]" 2>/dev/null || true)
         for inc in $includes; do
             if [[ -z "${ALL_COLLECTIONS[$inc]}" ]]; then
                 echo -e "${RED}❌ Error: Collection '$col' (in $manifest) includes missing collection '$inc'${NC}"
@@ -69,10 +69,10 @@ while read -r manifest; do
         done
 
         # Check Assets
-        count=$(yq e ".[\"$col\"].items | length" "$manifest")
+        count=$(cat "$manifest" | yq e ".[\"$col\"].items | length")
         if [ "$count" -gt 0 ]; then
             for ((i=0; i<count; i++)); do
-                src=$(yq e ".[\"$col\"].items[$i].src" "$manifest")
+                src=$(cat "$manifest" | yq e ".[\"$col\"].items[$i].src")
 
                 # Resolve Path
                 if [[ "$src" == /* ]]; then
@@ -93,7 +93,7 @@ while read -r manifest; do
                     FAILED=1
                 elif [ -d "$full_path" ]; then
                     # If src is a directory, dest MUST end with /
-                    dest=$(yq e ".[\"$col\"].items[$i].dest" "$manifest")
+                    dest=$(cat "$manifest" | yq e ".[\"$col\"].items[$i].dest")
                     if [[ "$dest" != */ ]]; then
                         echo -e "${RED}❌ Error: Collection '$col' item '$src' is a directory, so dest '$dest' must end with '/'${NC}"
                         FAILED=1