The package classicthesis was born when André Miede was writing is PhD thesis. He wanted to reproduce a style quite similar to Bringhurst's book “The Elements of Typographic Style” (with the obvious difference of the paper size).
At some point in time, it was suggested to him to lighten the package by placing calls to secondary packages in an auxiliary one, that he called classicthesis-ldpkg.
Later on, he decided to change the distribution, by removing the auxiliary package and providing (only in the documentation tree) a file called classicthesis-config.tex.
The choice of packages loaded by the auxiliary package/file is strictly tied to what Miede needed for his own thesis.
As it stands now, the file contains:
A call to inputenc, with the utf8 option
A set of options to be passed to classicthesis.sty
Some useless commands called \myTitle, \mySubtitle and so on, which Miede seems to be fond of
The definition of a dummy counter, which serves no purpose
The allocation of a length register, for unknown purposes
Some abbreviations for i. e. and e. g. (according to the German usage)
Some “handy” packages: babel, csquotes, biblatex, amsmath (with the fleqn option), fontenc, textcomp, scrhack, xspace, mparhack, fixltx2e, acronym, tabularx, caption, subfig, listings (with a long setup), graphicx (with the option pdftex, which is a big error), hyperref (with his preferred settings).
Finally, the file calls classicthesis.
Now, this way of doing is rather disputable. For instance, hyperref should be the last package called (with some exceptions). It should also be called after classicthesis (which also loads other packages).
As you see, some of the package loaded (point 7) are not needed by the vast majority of users. Some even select options that a user may not want.
According to the documentation, the current classicthesis-config.tex file is just a model that a user should modify. Well, the way the file is written is scaring, to say the least, the newbie. (And in some points it makes the expert smile.)
The best thing is to forget about it. Declare the class (scrbook) with the needed options, set the options for fontenc, inputenc and babel, then load classicthesis; after this call, load the packages you really require.
\includeto input a tex file in the preamble isn't correct. The warnings ... You get them with the standard template because the implemntatioon ofclassicthesis(the package) is just rubbish at times. – Johannes_B Feb 13 '16 at 13:42classicthesis-ldpkgand found one such file n github, clearly changed (great trend by the way, i love it). I don't know what is left from the original, but it feels a bit rigid. Like a grumpy old man sitting in a bar throwing peanuts on the new citizens in town. – Johannes_B Feb 13 '16 at 13:52classicthesis-config.texcoming with the distribution is just a collection of (badly called) packages with options that you'll probably won't need. Leave it alone. – egreg Feb 13 '16 at 13:57