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>

main-installer.sh

@@ -99,6 +99,9 @@ trap 'cleanup_on_error "$BASH_COMMAND"' ERR
 # Execute the installation steps in sequence
 log "INFO" "Starting installation process..."
 
+# Set default for TRANSMISSION_REMOTE
+export TRANSMISSION_REMOTE=false
+
 if [ "$IS_UPDATE" = true ]; then
   log "INFO" "Running in update mode - preserving existing configuration..."
   
@@ -132,10 +135,16 @@ else
   
   # Step 1: Gather configuration from user
   log "INFO" "Gathering configuration..."
-  gather_configuration || {
+  # Explicitly run this to ensure it's called before dependencies
+  set +e # Temporarily disable exit on error
+  if ! gather_configuration; then
     log "ERROR" "Configuration gathering failed"
     exit 1
-  }
+  fi
+  set -e # Re-enable exit on error
+  
+  # Debug: Verify TRANSMISSION_REMOTE is set
+  log "INFO" "After configuration gathering, TRANSMISSION_REMOTE=$TRANSMISSION_REMOTE"
   
   # Step 2: Install dependencies
   log "INFO" "Installing dependencies..."