If you ensure that everything that you want to be compiled is currently compiled, you can let https://github.com/emacscollective/auto-compile manage it from there.
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Quick pain-saver tip
Properly package that code (sounds like you're most of the way there) and let your package manager handle it.
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I simply use:
(defun my-recompile-init-eln ()
(interactive)
(byte-compile-file "~/.emacs.d/early-init.el")
(native-compile "~/.emacs.d/early-init.el")
(byte-compile-file "~/.emacs.d/init.el")
(native-compile "~/.emacs.d/init.el"))
I use it manually, but I don't care too much because I don't edit my init files too often anymore. But it shouldn't be too hard to run this function automatically at boot if the .elc
is outdated compared to the .el
.