Only keep multiple folders with same file name. Align is the reference folder.

script.sh

#!/bin/bash

# Define the path to your root folder
rootFolder="."

# Define the path to your input folder (folderA)
folderA="$rootFolder/align"

# Function to delete excess files and print file count
delete_excess_files () {
    local fileCount=0
    for file in "$1"/*; do
        # Increment file count
        ((fileCount++))
        filename=$(basename "$file")
        if [ ! -f "$folderA/$filename" ]; then
            echo "Deleting $file"
            rm "$file"
            ((fileCount--))
        fi
    done
    echo "Number of files remaining in $(basename "$1"): $fileCount"
}

# Loop through each folder in the root folder
for folder in "$rootFolder"/*; do
    # Check if it's a directory and not the input folder
    if [ -d "$folder" ] && [ "$(basename "$folder")" != "input" ]; then
        echo "Processing $folder"
        delete_excess_files "$folder"
    fi
done

echo "Processing complete."