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In default config-extensions.def, section [X] is followed by section [X_cfgBindings]. In user config-extensions.cfg, the two sections are written independently by the config dialog (key bindings) and by the extensions dialog (the [X]). While having [X] and [X_cfgBindings] separated and even reversed in order seems to still work, it would be nicer if they were written together in the proper order. It might be possible to do this in the user-config writing method in config-handler.

Need some clarification on this issue. I tried changing the cfgBindings for FormatParagraph. It creates a new key-set and writes the changes to user config-keys.cfg in ~/.idlerc(the keybindings). Any changes made to FormatParagraph in extension dialog(the [X]) are written to the user config-extensions.cfg file in ~/.idlerc.
Have I understood the issue correctly in saying that the desired outcome is both [X] and [X_cfgBindings] write to config-extensions.cfg in ~/.idlerc?

When I alter an *extension* key binding (in the keys page of idle pref dialog), the change shows up in .idlerc/config-extensions.cfg, not config-keys.cfg. For instance,
[ZoomHeight_cfgBindings]
zoom-height = <Control-Alt-Key-space>
If I also disable zoom-height, the following appears in a separate part of the same file.
[XoomHeight]
enable=False
For me, the two blocks are already in the same file. The same is true for FormatParagraph. I intended this issue to be about bringing them together in the file, with the [X] block first. You seem to be saying that the current behavior is different on linux. Since FormatParagraph is still special (see #20577), try ZoomHeight also.

ZoomHeight behavior on linux is as what you mentioned. Now I have understood this issue. Working on it.

#27099 (converting built-in extensions to features) made this less important. But it is still relevant to actual extensions. There is a dummy extension, zzdummy, for testing.