I have RNAseq libraries of 28 samples, and I got 2-4 fastq.gz files from each sample. I am just trying to figure out how to merge them.  I have already done what I feels is a due-diligence search of the bioconductor tutorials and google, and so far it appears that there is no way in r + windows to easily merge multiple fastq.gz files from the same sample into one fastq file containing all of the reads for that sample.  I don't think there should be any quality differences between the reads in these files because these are not technical replicates, the sequencing center just seems to format their data output to start a new fastq file whenever the previous one reaches 603.5 MB.  But I need to merge the ones pertaining to a single sample because all of the tools for downstream work all seem to assume that 1 fastq.gz file = 1 sample.  Is this true?

I suppose I could map each file individually to my reference genome, and then add the mapped counts from the fasta.gz files from the same sample together.  Is this what I am to infer I should do?  Or should I spend a day installing a linux virtual box simply so I can use its cat command?

I think you can use ShortRead::writeFastq() with argument mode="a" to append to an existing file. Is that what you mean by 'merge'? Maybe the idea would be (completely untested!)

fout = "combined.fastq"
fls = dir(pattern="fastq.gz")
for (fl in fls) {
    fq = readFastq(fl)
    writeFastq(fq, fout, mode="a", compress=TRUE)
}

You could use FastqStreamer() and yield() to avoid the need to read the entire fastq file into memory.