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Assuming the names of the files and directories follow the same naming convention in that they share some common grouping prefix followed by a dot, and assuming we don't know the filename suffixes of files or directories:

topdir=.

for dirname in "$topdir"/*/; do
    prefix=$( basename "$dirname" )  # ./FileC.directory/ --> FileC.directory
    prefix=${prefix%%.*}             # FileC.directory    --> FileC

    for filename in "$topdir/$prefix".*; do
        if [ ! -d "$filename" ]; then
            mv -i "$filename" "$dirname"
        fi
    done
done

The outer loop iterates over all directories in the directory $topdir (here set to ., the current directory). The $prefix will be the base name of the directory name, with the bit after the first dot removed.

Once the prefix has been computed, non-directories (files) in the same $topdir directory that share the same prefix are moved to the directory.