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I am using Vincet Goulet's modified version of Emacs that use site-start.el.

http://vgoulet.act.ulaval.ca/en/emacs/

I have read the description of its use but I don't understand exactly what conditions may affect choosing site-start.el over init.el. Can someone clarify a rule of thumb on this?

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    Type: M-x describe-variable RET site-run-file RET and take a look at the doc-string. If you wish to see at what location it is called in the startup process, type M-x find-library RET startup RET and search for the site-run-file references within the library. – lawlist Aug 6 '16 at 17:48
  • Could you provide a link for the Emacs version you're using? – lunaryorn Aug 6 '16 at 18:48
  • Is site-site.el a typo? – Stefan Aug 6 '16 at 19:20
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[The] init file [...] specifies how to initialize Emacs for you. [Therefore it is normally located in (a subdir of) your home directory.]
[You] may also have a site startup file [...] named site-start.el. [It is normally located] in a subdirectory named site-lisp in the Emacs installation directory, such as /usr/local/share/emacs/site-lisp [but] you can place [...] site-start.el in any of the directories which Emacs searches for Lisp libraries. [...] We recommend against using site-start.el for changes that some users may not like.

(see The Emacs Initialization File)

In a multi-user environment, as an admin, you put in site-start.el the customisations intended for all users, while single users will use their own init file.
Also, if you make a customised Emacs distro, you put specific distro packages, together with site-start.el, in the site-lisp directory.

Before the personal computing era, having a centralised Emacs server was a necessity due to the mainframe computing model, which required so called site customisations. A typical scenario nowadays is that each user has their own Emacs on their own computer, perhaps a laptop. Therefore there is not much need for site customisations, including site-start.el.

Anyway you might use Emacs as a daemon to manage your emails, you org agenda notifications, etc. In this case site-start.el is the proper place to craft your daemon.

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