Allow overriding completion in `auto_prepend_file`

Currently, it's possible to override `php -a`s completion
functionality to provide an alternative to the C implementation,
with `readline_completion_function()`.

However, that surprisingly gets overridden when called from
`auto_prepend_file`, because those scripts get run before the interactive shell
is started. I believe that not overriding it would be more consistent
with what happens when you override the completion function **after** the
interactive shell.

CLI is the only built-in API that uses this (See discussion in GH-5872).
I believe MINIT and RINIT will only run once when invoked with `php -a`.

Add documentation about the architecture of how php uses readline/libedit

Closes GH-5872

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