It looks like the -m flag takes an undocumented optional argument of a CSV file listing the chapter titles.
However, calling HandBrakeCLI with -m foo.csv doesn't cause foo.csv to get read (testing the 0.9.1 code on a Linux box running Centos 4). This appears to be because optarg is set to NULL when executing the case 'm' block.
A simple workaround that helped me was changing the string passed to getopt_long() to "[...]m:a[...]" instead of "[...]ma[...]". I suspect a more correct change would be to look at optind instead, but I'm not familiar with getopt() to see how.
The -m flag in HandBrakeCLI
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