Fix configuration gathering and order of operations

- Add emergency fallback to ask about remote Transmission if config step was skipped
- Add CONFIG_GATHERED flag to track if config step was run
- Improve bootstrap installer with clear explanation of what to expect
- Explicitly check for gather_configuration success and output debug info
- Add additional variable initialization to ensure consistent behavior

🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>

modules/config-module.sh

@@ -78,6 +78,9 @@ function gather_configuration() {
   
   # Initialize default values for Transmission mode
   export TRANSMISSION_REMOTE=false
+  
+  # Set flag to indicate that configuration was gathered
+  export CONFIG_GATHERED=true
   echo -e "${BOLD}Installation Configuration:${NC}"
   echo -e "Please provide the following configuration parameters:"
   echo

modules/dependencies-module.sh

@@ -12,6 +12,24 @@ function install_dependencies() {
   fi
   
   log "INFO" "Transmission mode: $([ "$TRANSMISSION_REMOTE" = true ] && echo "Remote" || echo "Local")"
+  
+  # Debug: print out whether the gather_configuration was called
+  if [ "$IS_UPDATE" != true ]; then
+    if [ -z "$CONFIG_GATHERED" ]; then
+      log "ERROR" "Configuration step was skipped! This is a bug."
+      log "INFO" "Please report this issue. Will now manually ask about Transmission location."
+      
+      # Emergency fix: Ask about remote installation here
+      read -p "Is Transmission running on a remote server? (y/n) [n]: " input_remote
+      if [[ $input_remote =~ ^[Yy]$ ]]; then
+        export TRANSMISSION_REMOTE=true
+        log "INFO" "Remote Transmission selected."
+      else
+        export TRANSMISSION_REMOTE=false
+        log "INFO" "Local Transmission selected."
+      fi
+    fi
+  fi
 
   # Check for package manager
   if command -v apt-get &> /dev/null; then