Support for comma-separated filenames

BACKGROUND/CURRENT ISSUE:
Currently the file delimiter is a comma, e.g. bowtie2 -1 flyA_1.fq,flyB_1.fq. Unfortunately, this means it is not possible to have file names containing commas(*). AFAIK, the only known workaround is to rename the files temporarily for passing them to bowtie2, which is rather tedious and makes log files referring to temporary filenames rather than the real ones.

REQUEST:
Alt 1: Add an option (e.g. --fsep <char>) to specify the file delimiter in file lists, e.g. bowtie2 --fsep ; -1 fly,A.fq;fly,B.fq
Alt 2: Support quoting of file names, e.g. bowtie2 -1 "fly,A.fq","fly,B.fq"
Alt 3: Support escaping commas in file names, e.g. bowtie2 -1 fly\,A.fq,fly\,B.fq
Alt 4: Add an option (e.g. --file1 <filename>) to specify a file containing rows of filenames, e.g. bowtie2 --file1 flyfiles.txt

FOOTNOTE:
(*) Commas are perfectly valid in filenames on "all" known/modern file system. For instance, it has been used by the CVS version control system for years. We also use it extensively in the Aroma Project [http://www.aroma-project.org/] to incorporate "tags" in filenames. See also http://en.wikipedia.org/wiki/Filename\).

Thanks,

Henrik Bengtsson (UCSF)