The permissions on the script files are set to be executable by everyone: -rwxr-xr-x
Thanks for the strace idea. I'm looking through the strace, but I haven't seen any helpful mention of the filter scripts yet. I've attached an abridged version of my strace with the middle of the file taken out. I don't know if this is helpful or not. I'll let you know if I solve the problem.
cgit.strace
Description: Binary data
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