Update deploy script: TM files from git, fix orphan containers

- Removed old import_reference_files.py step from --init (TM/ref files
  are now tracked in git, no separate import needed)
- Added file count verification during --init to confirm TM files arrived
- Added --remove-orphans to docker compose commands to prevent stale
  containers serving old builds
- Standard deploy now does compose down before up to ensure clean restart

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

deploy.sh

@@ -93,9 +93,9 @@ if [ "$INIT" = true ]; then
         log ".env already exists, skipping creation"
     fi
 
-    # Create storage directories
-    log "Creating storage directories..."
-    mkdir -p storage/amazon/{tm,ref}
+    # Storage directories are now tracked in git (storage/amazon/tm + ref)
+    # Just ensure the base directory exists for runtime uploads
+    mkdir -p storage
 
     # Build all images
     log "Building all Docker images (this may take a few minutes)..."
@@ -125,16 +125,13 @@ if [ "$INIT" = true ]; then
     log "Running database migrations..."
     $COMPOSE exec -T backend alembic upgrade head
 
-    # Import reference files (run on host since files are local)
-    if [ -d "../Agent build + supporting JSONs/JSON REFS and TMs" ]; then
-        log "Importing reference and TM files..."
-        python3 seed/import_reference_files.py \
-            --source "../Agent build + supporting JSONs/JSON REFS and TMs" \
-            --target storage/amazon
-    else
-        warn "Reference files source directory not found at ../Agent build + supporting JSONs/JSON REFS and TMs"
-        warn "You can import them manually later:"
-        warn "  python3 seed/import_reference_files.py --source /path/to/JSON_REFS_and_TMs --target storage/amazon"
+    # TM and reference files are now tracked in git — no import step needed.
+    # Verify they arrived via git pull:
+    TM_COUNT=$(find storage/amazon/tm -name '*.json' 2>/dev/null | wc -l)
+    REF_COUNT=$(find storage/amazon/ref -name '*.json' 2>/dev/null | wc -l)
+    log "Found $TM_COUNT TM files and $REF_COUNT reference files in storage/amazon/"
+    if [ "$TM_COUNT" -eq 0 ]; then
+        warn "No TM files found! Check that git pulled storage/amazon/tm/ correctly."
     fi
 
     # Seed database
@@ -144,7 +141,7 @@ if [ "$INIT" = true ]; then
 
     # Start all remaining services
     log "Starting all services..."
-    $COMPOSE up -d
+    $COMPOSE up -d --remove-orphans
 
     # ---------------------------------------------------------------
     # Apache configuration
@@ -240,8 +237,9 @@ $COMPOSE up -d backend
 sleep 5
 $COMPOSE exec -T backend alembic upgrade head
 
-# Restart all services
+# Restart all services (remove orphans to avoid stale containers)
 log "Restarting all services..."
+$COMPOSE down --remove-orphans
 $COMPOSE up -d
 
 # Health check