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Files generated by fresh are read-only to prevent accidental loss of changes.
Applications such Emacs and Irssi which write to their config files are unable to write to the read-only files generated by fresh. You can symlink these files directly out of your dotfiles in your freshrc:
# freshrc:
ln -sf ~/.dotfiles/emacs ~/.emacs
Can I conditionally include based on OS or host?
Yes. As fresh is written in shell-script, we can add conditionals using shell-script. See Scripting your freshrc file for details.