Agent config: avoid introducing unused arguments to new functions  #1621

Let's actually remove the always_run argument - it's always true.
And remove pass_filenames - it's always false.
And remove require_serial - it's unneeded when pass_filenames is false.

Originally posted by @nathanjmcdougall in #1606 (comment)

This is the YAGNI principle in action. We should create an agent skill which explains some principles of good function design. One of them is YAGNI for function arguments. We shouldn't pre-emptively introduce arguments unless they are needed at the UI level; or if they are helper/internal functions then we definitely shouldn't introduce arguments which are always passed with the same value/non-default values.