The configuration file count is very large, partly due to supporting so many features, partly because we have created smaller units of configuration dealing with specific tasks, and partly because we've tried to expose a lot of options directly without requiring code changes or plugins. In practice, you should expect to interact with the same files as in earlier versions on a regular basis and you may never touch many of these files.
As of V4.1, many of the smaller files have been removed by default for new installs and are copied into place only after enabling a corresponding Module. This reduces the number of files to deal with or to ignore when not using less common features. These files are no longer mentioned here but will be noted where necessary in the documentation of particular features.
To help orient you, a summary of the general function of each file follows along with a tip for when or why you might care about it. The order is alphabetic, not based on the frequency of use.
The "RL?" column notes which files can be reloadable, but not necessarily which ones are since that depends on the "checkInterval" properties in services.properties.