Problema con bibliografia e indice.

Gentili frequentatori del forum,
Ho deciso di scrivere la tesi in Latex ma ho riscontrato alcune difficoltà, vi spiego nella speranza che qualcuno sappia indicarmi il problema.
Da texmaker compilo 3 volte in modalità compilazione rapida il file mine. tex (principale) e poi do il makePDF sperando che con questa operazione mi compaia la bibbliografia.
A questo punto ottengo il PDF con l’indice compilato correttamente ma non la bibbliografia.
Decido di ricompialare altre tre volte e nuovamente lancio il comando make PDF.
Questa volta ottengo un file con la bibbliografia, ma nonostante mi rimangano le pagine dell’indice, di fatto l’indice sparisce e mi rimane solamente la pagina bianca con la sola intestazione.

aggiungo di seguito il file mine: `%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Classicthesis Typographic Thesis
% LaTeX Template
% Version 1.3 (15/2/14)
%
% This template has been downloaded from:
% http://www.LaTeXTemplates.com
%
% Original author:
% André Miede (http://www.miede.de)
%
% License:
% CC BY-NC-SA 3.0 (http://creativecommons.org/licenses/by-nc-sa/3.0/)
%
% General Tips:
% 1) Make sure to edit the classicthesis-config.file
% 2) New enumeration (A., B., C., etc in small caps): \begin{aenumerate} \end{aenumerate}
% 3) For margin notes: \marginpar or \graffito{}
% 4) Do not use bold fonts in this style, it is designed around them
% 5) Use tables as in the examples
% 6) See classicthesis-preamble.sty for useful commands
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%—————————————————————————————-
% PACKAGES AND OTHER DOCUMENT CONFIGURATIONS
%—————————————————————————————-

\documentclass[
twoside,openright,titlepage,numbers=noenddot,headinclude,%1headlines,
footinclude=true,cleardoublepage=empty,
BCOR=5mm,paper=a4,fontsize=12pt, % Binding correction, paper type and font size
italian % Languages
]{scrreprt}

% Includes the file which contains all the document configurations and packages – make sure to edit this file
% package italiano
\renewcommand{\contentsname}{Sommario}
\renewcommand{\listfigurename}{List of Figures}
\renewcommand{\listtablename}{List of Tables}
\renewcommand{\bibname}{Bibliografia}
\renewcommand{\indexname}{Indice}
\renewcommand{\figurename}{Figura}
\renewcommand{\tablename}{Tavola}
\renewcommand{\partname}{Parte}
\renewcommand{\chaptername}{Capitolo}
\renewcommand{\appendixname}{Appendice}
\renewcommand{\abstractname}{Abstract}
\renewcommand{\today}{\ifcase\month\or
Gennaio\or Febbraio\or Marzo\or Aprile\or Maggio\or Giugno\or
Luglio\or Agosto\or Settembre\or Ottobre\or Novembre\or Dicembre\fi
\space\number\day, \number\year}
\input{classicthesis-config}
\renewcommand{\finalVersionString}{}
\renewcommand{\PrelimText}{}
\begin{document}

\frenchspacing % Reduces space after periods to make text more compact

%\raggedbottom % Makes all pages the height of the text on that page

\selectlanguage{italian} % Select your default language – e.g. american or ngerman

%\renewcommand*{\bibname}{new name} % Uncomment to change the name of the bibliography
%\setbibpreamble{} % Uncomment to include a preamble to the bibliography – some text before the reference list starts

\pagenumbering{roman} % Roman page numbering prior to the start of the thesis content (i, ii, iii, etc)

\pagestyle{headings} % Suppress headers for the pre-content pages

%—————————————————————————————-
% PRE-CONTENT THESIS PAGES
%—————————————————————————————-

\include{FrontBackMatter/Titlepage} % Main title page

\include{FrontBackMatter/Titleback} % Back of the title page

%\cleardoublepage\include{FrontBackMatter/Dedication} % Dedication page

%\cleardoublepage\include{FrontBackMatter/Foreword} % Uncomment and create a Foreword.tex to include a foreword
\selectlanguage{italian}
%\cleardoublepage\include{FrontBackMatter/Abstract} % Abstract page

\cleardoublepage\include{FrontBackMatter/Prefazione} % Acknowledgements page

\cleardoublepage\include{FrontBackMatter/Ringraziamenti} % Acknowledgements page

\pagestyle{scrheadings} % Show chapter titles as headings

\cleardoublepage\include{FrontBackMatter/Contents} % Contents, list of figures/tables/listings and acronyms

\cleardoublepage

\pagenumbering{arabic} % Arabic page numbering for thesis content (1, 2, 3, etc)
%\setcounter{page}{90} % Uncomment to manually start the page counter at an arbitrary value (for example if you wish to count the pre-content pages in the page count)

\cleardoublepage % Avoids problems with pdfbookmark
%—————————————————————————————-
% VOCABOLARIO E SILLABAZIONI
%—————————————————————————————-
\hyphenation{li-mi-ti}
\hyphenation{per-met-te-re}
\hyphenation{na-vi-ga-zio-ne}

%—————————————————————————————-
% THESIS CONTENT – CHAPTERS
%—————————————————————————————-

\ctparttext{testo di prova} % Text on the Part 1 page describing the content in Part 1

\part{Alcuni concetti di base} % First part of the thesis
%
\include{capitoli/cap1/cap1} % Chapter 1 Anatomia e biomeccanica del ginocchio
\include{capitoli/cap2/cap2} % Chapter 2 Cinematica del ginocchio
\include{capitoli/cap3/cap3} % Chapter 3 Il legamento crociato anteriore (LCA)
\include{capitoli/cap5/cap5} % Chapter 5 Diagnosi della lesione del LCA
\include{capitoli/cap7/cap7} % Chapter 7 Trattamento chirurgico

\cleardoublepage % Empty page before the start of the next part

%————————————————

\ctparttext{You can put some informational part preamble text here. Illo principalmente su nos. Non message \emph{occidental} angloromanic da. Debitas effortio simplificate sia se, auxiliar summarios da que, se avantiate publicationes via. Pan in terra summarios, capital interlingua se que. Al via multo esser specimen, campo responder que da. Le usate medical addresses pro, europa origine sanctificate nos se.} % Text on the Part 2 page describing the content in Part 2

\part{La riabilitazione} % Second part of the thesis
\include{capitoli/cap4/cap4} % Chapter 4 Reabilitazione del ginocchio dopo la ricostruzione del LCA
%\include{Chapters/Chapter02} % Chapter 2
%\include{Chapters/Chapter03} % Chapter 3
%\include{Chapters/Chapter04} % Chapter 4 – empty template

%—————————————————————————————-
% THESIS CONTENT – APPENDICES
%—————————————————————————————-

%\appendix

%\part{Appendix} % New part of the thesis for the appendix

%\include{Chapters/Chapter0A} % Appendix A
%\include{Chapters/Chapter0B} % Appendix B – empty template

%—————————————————————————————-
% POST-CONTENT THESIS PAGES
%—————————————————————————————-

%\cleardoublepage\include{FrontBackMatter/Bibliography} % Bibliography

%\cleardoublepage\include{FrontBackMatter/Colophon} % Colophon

\bibliographystyle{unsrtnat} %apalike; (plainnat.bst, abbrvnat.bst e unsrtnat.bst)sostituiscono i corrispondenti stili standard di BibTEX (plain.bst, abbrv.bst e unsrt.bst)
\bibliography{bibliografia}

%—————————————————————————————-

\end{document}
`

Di seguito il file di configurazione con i pacchetti etc: `%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Thesis Configuration File
%
% The main lines to change in this file are in the DOCUMENT VARIABLES
% section, the rest of the file is for advanced configuration.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%—————————————————————————————-
% DOCUMENT VARIABLES
% Fill in the lines below toz enter your information into the thesis template
% Each of the commands can be cited anywhere in the thesis
%—————————————————————————————-

% Remove drafting to get rid of the '[ Date – classicthesis version 4.0 ]' text at the bottom of every page
\PassOptionsToPackage{eulerchapternumbers,listings,drafting, pdfspacing, subfig,beramono,eulermath,parts}{classicthesis}
% Available options: drafting parts nochapters linedheaders eulerchapternumbers beramono eulermath pdfspacing minionprospacing tocaligned dottedtoc manychapters listings floatperchapter subfig
% Adding 'dottedtoc' will make page numbers in the table of contents flushed right with dots leading to them

\newcommand{\myTitle}{tesi di laurea magistrale\xspace}
\newcommand{\mySubtitle}{L********e\xspace}
\newcommand{\myDegree}{Doktor-Ingenieur (Dr.-Ing.)\xspace}
\newcommand{\myName}{A*******\xspace}
\newcommand{\myProf}{L*******\xspace}
\newcommand{\myOtherProf}{Put name here\xspace}
\newcommand{\mySupervisor}{Put name here\xspace}
\newcommand{\myFaculty}{Put data here\xspace}
\newcommand{\myDepartment}{Put data here\xspace}
\newcommand{\myUni}{Put data here\xspace}
\newcommand{\myLocation}{Bologna\xspace}
\newcommand{\myTime}{Ottobre 2014\xspace}
\newcommand{\myVersion}{\xspace}

%—————————————————————————————-
% USEFUL COMMANDS
%—————————————————————————————-

\newcommand{\ie}{i.\,e.}
\newcommand{\Ie}{I.\,e.}
\newcommand{\eg}{e.\,g.}
\newcommand{\Eg}{E.\,g.}

\newcounter{dummy} % Necessary for correct hyperlinks (to index, bib, etc.)
\providecommand{\mLyX}{L\kern-.1667em\lower.25em\hbox{Y}\kern-.125emX\@}

%—————————————————————————————-
% PACKAGES
%—————————————————————————————-

\usepackage{lipsum} % Used for inserting dummy 'Lorem ipsum' text into the template
\usepackage{graphicx} %<--per le figure \usepackage[doublespacing]{setspace} % interlinea\singlespacing (interlinea singola), \onehalfspacing(interlinea 1,5) e \doublespacing (interlinea doppia). \usepackage[colorlinks=false]{hyperref}%<--inserisce segnalibri e riferimenti indice \usepackage[authoryear,square,numbers]{natbib} % for the bibliography \usepackage{varioref} %------------------------------------------------ \PassOptionsToPackage{latin9}{inputenc} % latin1 (ISO-8859-1) = latin1+"Euro sign" \usepackage{inputenc} %------------------------------------------------ %\PassOptionsToPackage{ngerman,american}{babel} % Change this to your language(s) % Spanish languages need extra options in order to work with this template %\PassOptionsToPackage{spanish,es-lcroman}{babel} \usepackage[italian]{babel} \selectlanguage{italian} %------------------------------------------------ \PassOptionsToPackage{square,numbers}{natbib} \usepackage{natbib} %------------------------------------------------ \PassOptionsToPackage{fleqn}{amsmath} % Math environments and more by the AMS \usepackage{amsmath} %------------------------------------------------ \PassOptionsToPackage{T1}{fontenc} % T2A for cyrillics \usepackage{fontenc} %------------------------------------------------ \usepackage{xspace} % To get the spacing after macros right %------------------------------------------------ \usepackage{mparhack} % To get marginpar right %------------------------------------------------ \usepackage{fixltx2e} % Fixes some LaTeX stuff %------------------------------------------------ \PassOptionsToPackage{smaller}{acronym} % Include printonlyused in the first bracket to only show acronyms used in the text \usepackage{acronym} % nice macros for handling all acronyms in the thesis %------------------------------------------------ %\renewcommand*{\acsfont}[1]{\textssc{#1}} % For MinionPro \renewcommand{\bflabel}[1]{{#1}\hfill} % Fix the list of acronyms %------------------------------------------------ \PassOptionsToPackage{pdftex}{graphicx} \usepackage{graphicx} %---------------------------------------------------------------------------------------- % FLOATS: TABLES, FIGURES AND CAPTIONS SETUP %---------------------------------------------------------------------------------------- \usepackage{tabularx} % Better tables \setlength{\extrarowheight}{3pt} % Increase table row height \newcommand{\tableheadline}[1]{\multicolumn{1}{c}{\spacedlowsmallcaps{#1}}} \newcommand{\myfloatalign}{\centering} % To be used with each float for alignment \usepackage{caption} \captionsetup{format=hang,font=small} \usepackage{subfig} %---------------------------------------------------------------------------------------- % CODE LISTINGS SETUP %---------------------------------------------------------------------------------------- \usepackage{listings} %\lstset{emph={trueIndex,root},emphstyle=\color{BlueViolet}}%\underbar} % for special keywords \lstset{language=[LaTeX]Tex, % Specify the language for listings here keywordstyle=\color{RoyalBlue}, % Add \bfseries for bold basicstyle=\small\ttfamily, % Makes listings a smaller font size and a different font %identifierstyle=\color{NavyBlue}, % Color of text inside brackets commentstyle=\color{Green}\ttfamily, % Color of comments stringstyle=\rmfamily, % Font type to use for strings numbers=left, % Change left to none to remove line numbers numberstyle=\scriptsize, % Font size of the line numbers stepnumber=5, % Increment of line numbers numbersep=8pt, % Distance of line numbers from code listing showstringspaces=false, % Sets whether spaces in strings should appear underlined breaklines=true, % Force the code to stay in the confines of the listing box %frameround=ftff, % Uncomment for rounded frame frame=single, % Frame border - none/leftline/topline/bottomline/lines/single/shadowbox/L belowcaptionskip=.75\baselineskip % Space after the "Listing #: Desciption" text and the listing box } %---------------------------------------------------------------------------------------- % HYPERREFERENCES %---------------------------------------------------------------------------------------- \PassOptionsToPackage{pdftex,hyperfootnotes=false,pdfpagelabels}{hyperref} \usepackage{hyperref} % backref linktocpage pagebackref \pdfcompresslevel=9 \pdfadjustspacing=1 \hypersetup{ % Uncomment the line below to remove all links (to references, figures, tables, etc) %draft, colorlinks=true, linktocpage=true, pdfstartpage=3, pdfstartview=FitV, % Uncomment the line below if you want to have black links (e.g. for printing black and white) %colorlinks=false, linktocpage=false, pdfborder={0 0 0}, pdfstartpage=3, pdfstartview=FitV, breaklinks=true, pdfpagemode=UseNone, pageanchor=true, pdfpagemode=UseOutlines, plainpages=false, bookmarksnumbered, bookmarksopen=true, bookmarksopenlevel=1, hypertexnames=true, pdfhighlight=/O, urlcolor=webbrown, linkcolor=RoyalBlue, citecolor=webgreen, %------------------------------------------------ % PDF file meta-information pdftitle={\myTitle}, pdfauthor={\textcopyright\ \myName, \myUni, \myFaculty}, pdfsubject={}, pdfkeywords={}, pdfcreator={pdfLaTeX}, pdfproducer={LaTeX with hyperref and classicthesis} %------------------------------------------------ } %---------------------------------------------------------------------------------------- % BACKREFERENCES %---------------------------------------------------------------------------------------- \usepackage{ifthen} % Allows the user of the \ifthenelse command \newboolean{enable-backrefs} % Variable to enable backrefs in the bibliography \setboolean{enable-backrefs}{false} % Variable value: true or false \newcommand{\backrefnotcitedstring}{\relax} % (Not cited.) \newcommand{\backrefcitedsinglestring}[1]{(Cited on page~#1.)} \newcommand{\backrefcitedmultistring}[1]{(Cited on pages~#1.)} \ifthenelse{\boolean{enable-backrefs}} % If backrefs were enabled { \PassOptionsToPackage{hyperpageref}{backref} \usepackage{backref} % to be loaded after hyperref package \renewcommand{\backreftwosep}{ and~} % separate 2 pages \renewcommand{\backreflastsep}{, and~} % separate last of longer list \renewcommand*{\backref}[1]{} % disable standard \renewcommand*{\backrefalt}[4]{% detailed backref \ifcase #1 \backrefnotcitedstring \or \backrefcitedsinglestring{#2} \else \backrefcitedmultistring{#2} \fi} }{\relax} %---------------------------------------------------------------------------------------- % AUTOREFERENCES SETUP % Redefines how references in text are prefaced for different % languages (e.g. "Section 1.2" or "section 1.2") %---------------------------------------------------------------------------------------- \makeatletter \@ifpackageloaded{babel} { \addto\extrasamerican{ \renewcommand*{\figureautorefname}{Figure} \renewcommand*{\tableautorefname}{Table} \renewcommand*{\partautorefname}{Part} \renewcommand*{\chapterautorefname}{Chapter} \renewcommand*{\sectionautorefname}{Section} \renewcommand*{\subsectionautorefname}{Section} \renewcommand*{\subsubsectionautorefname}{Section} } \addto\extrasngerman{ \renewcommand*{\paragraphautorefname}{Absatz} \renewcommand*{\subparagraphautorefname}{Unterabsatz} \renewcommand*{\footnoteautorefname}{Fu\"snote} \renewcommand*{\FancyVerbLineautorefname}{Zeile} \renewcommand*{\theoremautorefname}{Theorem} \renewcommand*{\appendixautorefname}{Anhang} \renewcommand*{\equationautorefname}{Gleichung} \renewcommand*{\itemautorefname}{Punkt} } \providecommand{\subfigureautorefname}{\figureautorefname} % Fix to getting autorefs for subfigures right }{\relax} \makeatother %---------------------------------------------------------------------------------------- \usepackage{classicthesis} %---------------------------------------------------------------------------------------- % CHANGING TEXT AREA %---------------------------------------------------------------------------------------- %\linespread{1.05} % a bit more for Palatino %\areaset[current]{312pt}{761pt} % 686 (factor 2.2) + 33 head + 42 head \the\footskip %\setlength{\marginparwidth}{7em}% %\setlength{\marginparsep}{2em}% %---------------------------------------------------------------------------------------- % USING DIFFERENT FONTS %---------------------------------------------------------------------------------------- %\usepackage[oldstylenums]{kpfonts} % oldstyle notextcomp %\usepackage[osf]{libertine} %\usepackage{hfoldsty} % Computer Modern with osf %\usepackage[light,condensed,math]{iwona} %\renewcommand{\sfdefault}{iwona} %\usepackage{lmodern} % <-- no osf support :-( %\usepackage[urw-garamond]{mathdesign} <-- no osf support :-( %\usepackage{newtxtext,newtxmath} %times matematica %\usepackage{mathptmx} %font times new roman %\usepackage{times}\renewcommand\rmdefault{stb}` Ringrazio anticipatamente, anche perché la consultazione del forum mi è già stata utile in diverse occasioni :wink: . Un saluto da Alessandro