reorganize rst files

Author: cliffckerr

README.rst

@@ -34,14 +34,16 @@ GitHub_ page. Full information about Covasim is provided in the documentation_.
 Background
 ==========
 
-Covasim has been used for analyses in over a dozen countries, both to inform policy decisions (including in the US, UK, and Australia), and as part of research studies. Academic papers that have been written using Covasim include:
+Covasim has been used for analyses in over a dozen countries, both to inform policy decisions (including in the US, UK, and Australia), and as part of research studies. Some key papers that have been written using Covasim include:
 
 1. **Controlling COVID-19 via test-trace-quarantine**. Kerr CC, Mistry D, Stuart RM, Rosenfeld R, Hart G, Núñez RC, Selvaraj P, Cohen JA, Abeysuriya RG, George L, Hagedorn B, Jastrzębski M, Fagalde M, Duchin J, Famulare M, Klein DJ (2021). *Nature Communications* 12:2993. doi: https://doi.org/10.1038/s41467-021-23276-9.
 
 2. **Determining the optimal strategy for reopening schools, the impact of test and trace interventions, and the risk of occurrence of a second COVID-19 epidemic wave in the UK: a modelling study**. Panovska-Griffiths J, Kerr CC, Stuart RM, Mistry D, Klein DJ, Viner R, Bonnell C (2020-08-03). *Lancet Child and Adolescent Health* S2352-4642(20) 30250-9. doi: https://doi.org/10.1016/S2352-4642(20)30250-9.
 
 3. **Estimating and mitigating the risk of COVID-19 epidemic rebound associated with reopening of international borders in Vietnam: a modelling study**. Pham QD, Stuart RM, Nguyen TV, Luong QC, Tran DQ, Phan LT, Dang TQ, Tran DN, Mistry D, Klein DJ, Abeysuriya RG, Oron AP, Kerr CC (2021-04-12). *Lancet Global Health* S2214-109X(21) 00103-0; doi: https://doi.org/10.1016/S2214-109X(21)00103-0.
 
+More complete lists of papers are given in ``papers.rst`` and ``papers.bib``.
+
 4. **Modelling the impact of reducing control measures on the COVID-19 pandemic in a low transmission setting**. Scott N, Palmer A, Delport D, Abeysuriya RG, Stuart RM, Kerr CC, Mistry D, Klein DJ, Sacks-Davis R, Heath K, Hainsworth S, Pedrana A, Stoove M, Wilson DP, Hellard M (in press; accepted 2020-09-02). *Medical Journal of Australia* [`Preprint <https://www.mja.com.au/journal/2020/modelling-impact-reducing-control-measures-covid-19-pandemic-low-transmission-setting>`__]; doi: https://doi.org/10.1101/2020.06.11.20127027.
 
 5. **The role of masks, testing and contact tracing in preventing COVID-19 resurgences: a case study from New South Wales, Australia**. Stuart RM, Abeysuriya RG, Kerr CC, Mistry D, Klein DJ, Gray R, Hellard M, Scott N (in press; accepted 2021-03-19). *BMJ Open*; doi: https://doi.org/10.1101/2020.09.02.20186742.
@@ -212,9 +214,7 @@ Licensing information and legal notices.
 Tests
 -----
 
-Integration, development, and unit tests. While not (yet) beautifully curated, these folders contain many usage examples. See the `tests README`_ for more information.
-
-.. _tests README: ./tests
+Integration, development, and unit tests. While not (yet) beautifully curated, these folders contain many usage examples. See README in the tests folder for more information.
 
 
 Disclaimer

CODE_OF_CONDUCT.rst code_of_conduct.rst

@@ -1 +1 @@
-.. include:: ../CODE_OF_CONDUCT.rst
+.. include:: ../code_of_conduct.rst

CONTRIBUTING.rst contributing.rst

@@ -1 +1 @@
-.. include:: ../CONTRIBUTING.rst
+.. include:: ../contributing.rst

docs/conduct.rst

@@ -1 +1 @@
-.. include:: ../FAQ.rst
+.. include:: ../faq.rst

docs/contributing.rst

@@ -1 +1 @@
-.. include:: ../GLOSSARY.rst
+.. include:: ../glossary.rst

docs/faq.rst

@@ -1 +1 @@
-.. include:: ../STYLE_GUIDE.rst
+.. include:: ../style_guide.rst