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@@ -1,126 +1,39 @@
   <ul>
-  <li>Introduction</li>
+  <li><a href="./1_Introduction/1_Intro.html#interacting-quantum-many-body-systems">Introduction</a></li>
     <ul>
     <li><a href="./1_Introduction/1_Intro.html#interacting-quantum-many-body-systems">Interacting Quantum Many Body Systems</a></li>
     <li><a href="./1_Introduction/1_Intro.html#mott-insulators">Mott Insulators</a></li>
     <li><a href="./1_Introduction/1_Intro.html#quantum-spin-liquids">Quantum Spin Liquids</a></li>
     <li><a href="./1_Introduction/1_Intro.html#outline">Outline</a></li>
   </ul>
-  <li>Background</li>
+  <li><a href="./2_Background/2.1_FK_Model.html#the-falikov-kimball-model">Background</a></li>
     <ul>
     <li><a href="./2_Background/2.1_FK_Model.html#the-falikov-kimball-model">The Falikov Kimball Model</a></li>
-      <ul>
-      <li><a href="./2_Background/2.1_FK_Model.html#the-model">The Model</a></li>
-      <li><a href="./2_Background/2.1_FK_Model.html#phase-diagram">Phase Diagram</a></li>
-      <li><a href="./2_Background/2.1_FK_Model.html#long-range-ising-models">Long Range Ising Models</a></li>
-    </ul>
     <li><a href="./2_Background/2.2_HKM_Model.html#the-kitaev-honeycomb-model">The Kitaev Honeycomb Model</a></li>
-      <ul>
-      <li><a href="./2_Background/2.2_HKM_Model.html#the-model">The Model</a></li>
-      <li><a href="./2_Background/2.2_HKM_Model.html#a-mapping-to-majorana-fermions">A mapping to Majorana Fermions</a></li>
-      <li><a href="./2_Background/2.2_HKM_Model.html#gauge-fields">Gauge Fields</a></li>
-      <li><a href="./2_Background/2.2_HKM_Model.html#anyons,-topology-and-the-chern-number">Anyons, Topology and the Chern number</a></li>
-      <li><a href="./2_Background/2.2_HKM_Model.html#phase-diagram">Phase Diagram</a></li>
-    </ul>
     <li><a href="./2_Background/2.3_Disorder.html#disorder-&-localisation">Disorder & Localisation</a></li>
-      <ul>
-      <li><a href="./2_Background/2.3_Disorder.html#localisation:-anderson,-many-body-and-disorder-free">Localisation: Anderson, Many Body and Disorder-Free</a></li>
-      <li><a href="./2_Background/2.3_Disorder.html#disorder-and-spin-liquids">Disorder and Spin liquids</a></li>
-      <li><a href="./2_Background/2.3_Disorder.html#amorphous-magnetism">Amorphous Magnetism</a></li>
-  </ul></ul>
-  <li>Chapter 3: The Long Range Falikov-Kimball Model</li>
-      <ul><ul>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.1_LRFK_Model.html#chapter-summary">Chapter Summary</a></li>
-    </ul>
+  </ul>
+  <li><a href="./3_Long_Range_Falikov_Kimball/3.1_LRFK_Model.html#chapter-summary">Chapter 3: The Long Range Falikov-Kimball Model</a></li>
+    <ul>
     <li><a href="./3_Long_Range_Falikov_Kimball/3.1_LRFK_Model.html#the-model">The Model</a></li>
-      <ul>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.1_LRFK_Model.html#localisation">Localisation</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.1_LRFK_Model.html#falikov-kimball-and-hubbard-models">Falikov Kimball and Hubbard models</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.1_LRFK_Model.html#long-ranged-ising-model">Long Ranged Ising model</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.1_LRFK_Model.html#localisation">Localisation</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.1_LRFK_Model.html#introduction">Introduction</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.1_LRFK_Model.html#the-long-ranged-falikov-kimball-model">The Long-Ranged Falikov-Kimball Model</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.1_LRFK_Model.html#introduction-and-motivation">Introduction and Motivation</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.1_LRFK_Model.html#literature-review">Literature Review</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.1_LRFK_Model.html#the-falikov-kimball-model">The Falikov-Kimball model</a></li>
-    </ul>
     <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#markov-chain-monte-carlo">Markov Chain Monte Carlo</a></li>
-      <ul>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#sampling">Sampling</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#markov-chains">Markov Chains</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#application-to-the-fk-model">Application to the FK Model</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#the-metropolis-hasting-algorithm">The Metropolis-Hasting Algorithm</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#metropolis-hastings">Metropolis-Hastings</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#convergence,-auto-correlation-and-binning">Convergence, Auto-correlation and Binning</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#applying-mcmc-to-the-fk-model">Applying MCMC to the FK model</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#proposal-distributions">Proposal Distributions</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#perturbation-mcmc">Perturbation MCMC</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#scaling">Scaling</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#binder-cumulants">Binder Cumulants</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#markov-chain-monte-carlo-in-practice">Markov Chain Monte-Carlo in Practice</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#two-step-trick">Two Step Trick</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#detailed-balance-for-the-two-step-method">Detailed Balance for the two step method</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#diagnostics-of-localisation">Diagnostics of Localisation</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#markov-chain-monte-carlo">Markov Chain Monte-Carlo</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#convergence-time">Convergence Time</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#auto-correlation-time">Auto-correlation Time</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#the-metropolis-hastings-algorithm">The Metropolis-Hastings Algorithm</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#choosing-the-proposal-distribution">Choosing the proposal distribution</a></li>
-      <li><a href="./3_Long_Range_Falikov_Kimball/3.2_LRFK_Methods.html#two-step-trick">Two Step Trick</a></li>
-    </ul>
     <li><a href="./3_Long_Range_Falikov_Kimball/3.3_LRFK_Results.html#the-phase-diagram">The Phase Diagram</a></li>
     <li><a href="./3_Long_Range_Falikov_Kimball/3.3_LRFK_Results.html#localisation-properties">Localisation Properties</a></li>
     <li><a href="./3_Long_Range_Falikov_Kimball/3.3_LRFK_Results.html#discussion-&-conclusion">Discussion & Conclusion</a></li>
     <li><a href="./3_Long_Range_Falikov_Kimball/3.3_LRFK_Results.html#acknowledgments">Acknowledgments</a></li>
     <li><a href="./3_Long_Range_Falikov_Kimball/3.3_LRFK_Results.html#[]{#app:disorder_model-label="app:disorder_model"}-uncorrelated-disorder-model">[]{#app:disorder_model label="app:disorder_model"} UNCORRELATED DISORDER MODEL</a></li>
   </ul>
-  <li>Chapter 4: The Amorphous Kitaev Model</li>
-      <ul><ul>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.1.2_AMK_Model.html#gauge-fields">Gauge Fields</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.1.2_AMK_Model.html#the-projector">The Projector</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.1.2_AMK_Model.html#the-ground-state">The Ground State</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.1.2_AMK_Model.html#phases-of-the-kitaev-model">Phases of the Kitaev Model</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.1.2_AMK_Model.html#what-is-so-great-about-two-dimensions?">What is so great about two dimensions?</a></li>
-    </ul>
+  <li><a href="./4_Amorphous_Kitaev_Model/4.1.2_AMK_Model.html#gauge-fields">Chapter 4: The Amorphous Kitaev Model</a></li>
+    <ul>
     <li><a href="./4_Amorphous_Kitaev_Model/4.1_AMK_Model.html#contributions">Contributions</a></li>
     <li><a href="./4_Amorphous_Kitaev_Model/4.1_AMK_Model.html#introduction">Introduction</a></li>
-      <ul>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.1_AMK_Model.html#amorphous-systems">Amorphous Systems</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.1_AMK_Model.html#glossary">Glossary</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.1_AMK_Model.html#the-kitaev-model">The Kitaev Model</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.1_AMK_Model.html#the-majorana-hamiltonian">The Majorana Hamiltonian</a></li>
-    </ul>
     <li><a href="./4_Amorphous_Kitaev_Model/4.2_AMK_Methods.html#methods">Methods</a></li>
-      <ul>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.2_AMK_Methods.html#voronisation">Voronisation</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.2_AMK_Methods.html#graph-representation">Graph Representation</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.2_AMK_Methods.html#colouring-the-bonds">Colouring the Bonds</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.2_AMK_Methods.html#mapping-between-flux-sectors-and-bond-sectors">Mapping between flux sectors and bond sectors</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.2_AMK_Methods.html#chern-markers">Chern Markers</a></li>
-    </ul>
     <li><a href="./4_Amorphous_Kitaev_Model/4.3_AMK_Results.html#results">Results</a></li>
-      <ul>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.3_AMK_Results.html#the-ground-state-flux-sector">The Ground State Flux Sector</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.3_AMK_Results.html#spontaneous-chiral-symmetry-breaking">Spontaneous Chiral Symmetry Breaking</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.3_AMK_Results.html#ground-state-phase-diagram">Ground State Phase Diagram</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.3_AMK_Results.html#anderson-transition-to-a-thermal-metal">Anderson Transition to a Thermal Metal</a></li>
-    </ul>
     <li><a href="./4_Amorphous_Kitaev_Model/4.3_AMK_Results.html#conclusion">Conclusion</a></li>
     <li><a href="./4_Amorphous_Kitaev_Model/4.3_AMK_Results.html#discussion">Discussion</a></li>
-      <ul>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.3_AMK_Results.html#limits-of-the-ground-state-conjecture">Limits of the ground state conjecture</a></li>
-    </ul>
     <li><a href="./4_Amorphous_Kitaev_Model/4.3_AMK_Results.html#outlook">Outlook</a></li>
-      <ul>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.3_AMK_Results.html#experimental-realisations-and-signatures">Experimental Realisations and Signatures</a></li>
-      <li><a href="./4_Amorphous_Kitaev_Model/4.3_AMK_Results.html#generalisations">Generalisations</a></li>
-  </ul></ul>
-  <li>Conclusion</li>
-      <ul><ul>
-      <li><a href="./5_Conclusion/5_Conclusion.html#discussion">Discussion</a></li>
-      <li><a href="./5_Conclusion/5_Conclusion.html#outlook">Outlook</a></li>
-  </ul></ul>
-  <li>Appendices</li>
+  </ul>
+  <li><a href="./5_Conclusion/5_Conclusion.html#discussion">Conclusion</a></li>
+  <li><a href="./6_Appendices/A.1_Markov_Chain_Monte_Carlo.html#markov-chain-monte-carlo">Appendices</a></li>
     <ul>
     <li><a href="./6_Appendices/A.1_Markov_Chain_Monte_Carlo.html#markov-chain-monte-carlo">Markov Chain Monte Carlo</a></li>
     <li><a href="./6_Appendices/A.2_Lattice_Generation.html#lattice-generation">Lattice Generation</a></li>