diff --git a/analysis/generate-manifest.sh b/analysis/generate-manifest.sh
index a4b7151..09cf527 100755
--- a/analysis/generate-manifest.sh
+++ b/analysis/generate-manifest.sh
@@ -80,7 +80,18 @@ extract_category() {
     else
         local rel="${path#$WORKSPACE_ROOT/}"
         local first_component="${rel%%/*}"
-        echo "$first_component"
+        # For @ts/, go one level deeper to get namespace (e.g., @ts/@auth)
+        if [[ "$first_component" == "@ts" ]]; then
+            local rest="${rel#*/}"
+            local second_component="${rest%%/*}"
+            if [[ -n "$second_component" && "$second_component" != "$rest" ]]; then
+                echo "@ts/$second_component"
+            else
+                echo "@ts"
+            fi
+        else
+            echo "$first_component"
+        fi
     fi
 }
 
@@ -205,43 +216,38 @@ find_python_packages() {
 detect_language_pairs() {
     log "🔗 Detecting language pairs..."
 
-    # Build map of directory names to packages
-    # For the new structure, TypeScript packages are in @ts/<name>/ and Python in @py/<name>/
-    declare -A TS_BY_DIR=()
-    declare -A PY_BY_DIR=()
+    # Name-based matching: normalize package names and find overlaps
+    # TS: strip scope prefix (@lilith/foo → foo)
+    # Python: strip lilith- prefix (lilith-foo → foo)
+    declare -A TS_BY_BASENAME=()
+    declare -A PY_BY_BASENAME=()
 
     for name in "${!TS_PACKAGES[@]}"; do
         IFS='|' read -r version description category path should_publish source <<< "${TS_PACKAGES[$name]}"
-        # Only consider packages in @ts/ directory
-        if [[ "$path" == *"/@ts/"* ]]; then
-            local dir_name
-            dir_name=$(extract_dir_name "$path")
-            TS_BY_DIR["$dir_name"]="$name|$version"
-        fi
+        # Strip scope: @lilith/queue → queue, @transftw/foo → foo
+        local base_name="${name#@*/}"
+        TS_BY_BASENAME["$base_name"]="$name|$version"
     done
 
     for name in "${!PY_PACKAGES[@]}"; do
         IFS='|' read -r version description category path source <<< "${PY_PACKAGES[$name]}"
-        # Only consider packages in @py/ directory
-        if [[ "$path" == *"/@py/"* ]]; then
-            local dir_name
-            dir_name=$(extract_dir_name "$path")
-            PY_BY_DIR["$dir_name"]="$name|$version"
-        fi
+        # Strip lilith- prefix: lilith-queue → queue
+        local base_name="${name#lilith-}"
+        PY_BY_BASENAME["$base_name"]="$name|$version"
     done
 
-    # Find pairs by matching directory names between @ts/ and @py/
-    for dir_name in "${!TS_BY_DIR[@]}"; do
-        if [[ -n "${PY_BY_DIR[$dir_name]:-}" ]]; then
-            IFS='|' read -r ts_name ts_version <<< "${TS_BY_DIR[$dir_name]}"
-            IFS='|' read -r py_name py_version <<< "${PY_BY_DIR[$dir_name]}"
+    # Find pairs by matching normalized base names
+    for base_name in "${!TS_BY_BASENAME[@]}"; do
+        if [[ -n "${PY_BY_BASENAME[$base_name]:-}" ]]; then
+            IFS='|' read -r ts_name ts_version <<< "${TS_BY_BASENAME[$base_name]}"
+            IFS='|' read -r py_name py_version <<< "${PY_BY_BASENAME[$base_name]}"
 
             local sync_type="loose"
-            if is_strict_sync "$dir_name"; then
+            if is_strict_sync "$base_name"; then
                 sync_type="strict"
             fi
 
-            PAIRS["$dir_name"]="$ts_name|$ts_version|$py_name|$py_version|$sync_type"
+            PAIRS["$base_name"]="$ts_name|$ts_version|$py_name|$py_version|$sync_type"
         fi
     done