Customization variables in `custom.el` are overwritten

[systemcrafters]

Customization variables in `custom.el` are overwritten

[jeffbowman]

I tested several ways to make sure that didn't happen ... bummer ! (facepalm!!)

custom-save-delete only deletes the values out of the buffer. It depends on them already being set beforehand. If they aren't, then they disappear, which is not intended (aka "bad"). Ultimately, we don't really need to call customize-save-customized at all, that was an attempt to get the currently customized values set during initialization stored in the custom-set-variables form. Your refactor works because it doesn't save the customized values (which is fine, they are in the "SET but not saved" state), and then we load the values set through the Customize UI, via Org Mode Agenda file manipulation, and/or from .dir-locals.el settings (ie, pressing the ! to accept and remember the settings (see discussion in #111). In the end, all we need to do is remove the call to customize-save-customized and add your better wording in the README.org.

We don't technically need to load the file in the after-init-hook, but that seemed like a reasonable place to put it so a user could choose to remove that from the hook if they don't want the custom-file loaded at all. The only (minor/nit picky) issue I have with your refactor is the use of lambda in the after-init-hook which makes it difficult to undo later.

Would you mind updating your PR to only remove the call to customized-save-customized? (I've added some review notes)

Thanks very much, great catch!