Atom spec parsing eats following file path.

[Tom Goddard]

Parsing does not work for a command requiring an atom spec followed by a file path if the file path starts with /. Get a "Missing required argument path" error apparently because the atom spec parsing consumed the file path perhaps thinking it is a chain id.

test #1 /tmp/this

-> Missing required argument path.

Test code is attached.

This is not a contrived example. I encountered this bug making a command called "imodcopies" that makes copies of a map (first arg) using matrices specified in a file (second arg).

Quoting the second argument works, but a user would never figure that out.

[Conrad Huang]

I think the conclusion we reached is that a filename is either the first argument to a command or must be preceded by a keyword. Examples of the former: "save" and "distance save"; examples of the latter: "clashes" and "movie encode".