In particular, because my shell script isn't the stock #!/usr/local/bin/fossil example, I can't pass the repository or directory options so it knows where to look for its data. An example in the cookbook writes a temporary compatible script containing the needed options and spawns an instance, but surely there has to be a better way.

Can "fossil cgi" accept -r or -d options that correspond to the "repository:" or "directory:" values from the shell script, or perhaps use a single switch and intelligently set the right value? For instance:

fossil cgi -r /home/fossil/myproject.fossil fossil cgi -d /home/fossil

Or maybe something like:

fossil -t /home/fossil/myproject.fossil fossil -t /home/fossil

where "-t" means "target" and sets the correct option based on whether the target is a file or directory.