Is it possible somehow to do a general configuration for Eleventy so that 'my_file.html' in the input folder ends up just as 'my_file.html' in the _site folder, not '/my_file/index.html'?
I know I can do it on a file by file basis with permalinks. But I'd like it configured for the site as a whole, if possible.
Unfortunately, since this behavior isn't encouraged, there isn't a simple configuration option to disable the directory output.
However, since permalink is part of the data cascade, you can set a global default, and in combination with the filePathStem computed data, you can set the output to be .html files.
To set a permalink using a global data file, add a permalink.js file to your global _data directory.
// _data/permalink.js
module.exports = '/{{ page.filePathStem }}.html'
There is also a config global data option coming soon to v1.0.0. I am not sure if it will handle the {{ page.filePathStep }} preprocessing, but if it does, that could be an option too, especially since it will keep config-related things inside the config file.
Yes, you can control where Eleventy writes things out by specifying a permalink value in the front matter. This is covered here: https://www.11ty.dev/docs/permalinks/#remapping-output-(permalink)
An example would be:
---
permalink: "/my_file.html"
---