Improve directory structure for temporary multiplexed files

[mikej888]

When processing multiplexed files, the following temporary files are created in <TMP_DIR>/ (where <FASTQ_FILE_NAME_PREFIX> is the name of a multiplexed file (without path or extension) defined in multiplex_fq_files):

<FASTQ_FILE_NAME_PREFIX>_trim.fq
<FASTQ_FILE_NAME_PREFIX>_extract_trim.fq
<FASTQ_FILE_NAME_PREFIX>_deplex/
    num_reads.tsv
    <TAG>.fastq
    ...
    Unassigned.fastq

Refactor multiplexing to instead create a <TMP_DIR>/<FASTQ_FILE_NAME_PREFIX> directory, with files with less verbose names, and more consistent with sample-specific temporary files:

trim.fq
extract_trim.fq
deplex/
    num_reads.tsv
    <TAG>.fastq
    ...
    Unassigned.fastq

[mikej888]

This issue goes away if #324 is done.