Clean up and update README.md (#4)

* point to readthedocs instead of embedded eccov4.pdf
* use relative links for repo directories
* improve organization and titles

README.md

@@ -1,26 +1,29 @@
 # ECCO v4 r2
 
-[This repository][] contains model settings ([code][], [input][]) and guidelines ([eccov4.pdf][]) which allow users to re-run the ECCO v4 r2 ocean state estimate using the [MITgcm][] and e.g. their on-premise cluster. An automated recipe for use with [Amazon Web Services' cfncluster][] is also provided here in the [example_scripts][] directory. For user support, if needed, contact <mitgcm-support@mit.edu> or <ecco-support@mit.edu>. Citation for this repository: 
+**Content:**
+
+This repository contains model settings ([code/](code/), [input/](input/)) and guidelines ([readthedocs](http://eccov4.readthedocs.io/en/latest/)) which allow users to re-run the ECCO v4 r2 ocean state estimate using the [MITgcm](http://mitgcm.org/) using on-premise cluster or using [Amazon Web Services' cfncluster][] via shell scripts provided in [example_scripts/](example_scripts/). If user support is needed, please contact <mitgcm-support@mit.edu> or <ecco-support@mit.edu>
+
+**Citation for this repository:**
 
 [![DOI](https://zenodo.org/badge/76184688.svg)](https://zenodo.org/badge/latestdoi/76184688)
 
-[This repository]: https://github.com/gaelforget/ECCO_v4_r2/
-[code]: https://github.com/gaelforget/ECCO_v4_r2/tree/master/code
-[input]: https://github.com/gaelforget/ECCO_v4_r2/tree/master/input
-[eccov4.pdf]: https://github.com/gaelforget/ECCO_v4_r2/blob/master/eccov4.pdf
-[example_scripts]: https://github.com/gaelforget/ECCO_v4_r2/tree/master/example_scripts
 [Estimating the Circulation and Climate of the Ocean]: http://ecco-group.org/
 [MIT general circulation model]: http://mitgcm.org/
-[MITgcm]: http://mitgcm.org/
 [Amazon Web Services' cfncluster]: https://aws.amazon.com/hpc/cfncluster/
 [the Harvard dataverse]: https://dataverse.harvard.edu/dataverse/ECCOv4r2
 [gcmfaces]: https://github.com/gaelforget/gcmfaces
 [MITprof]: https://github.com/gaelforget/MITprof
+[the ECCO servers]: http://ecco-group.org/products.htm
+[direct download]: https://dspace.mit.edu/bitstream/handle/1721.1/102062/standardAnalysis.pdf
+
+**ECCO v4 r2:** 
 
-**ECCO v4 r2** ([Estimating the Circulation and Climate of the Ocean][], version 4, release 2) is an ocean state estimate and solution of the MITgcm ([MIT general circulation model][]) that covers the period from 1992 to 2011 (Forget et al., 2016). It is a minor update of the original ECCO v4 solution (Forget et al., 2015) that benefits from a few additional corrections listed in Forget et al. (2016) and is easier to analyze and re-run. Its input and output are distributed via <http://ecco-group.org/products.htm> and permanently archived via [the Harvard dataverse][]. They can be analyzed and manipulated using e.g. the [gcmfaces][] and [MITprof][] Matlab toolboxes.
+[Estimating the Circulation and Climate of the Ocean][], version 4, release 2 (ECCO v4 r2) is an ocean state estimate and solution of the [MIT general circulation model][] that covers the period from 1992 to 2011 (Forget et al., 2016). It is a minor update of the original ECCO v4 solution (Forget et al., 2015) that benefits from a few additional corrections listed in Forget et al. (2016) and is easier to analyze and re-run. Its input and output are distributed via [the ECCO servers][] and permanently archived via [the Harvard dataverse][]. They can be analyzed and manipulated using e.g. the [gcmfaces][] and [MITprof][] Matlab toolboxes.
 
+**References:**
 
-Forget, G., J.-M. Campin, P. Heimbach, C. N. Hill, R. M. Ponte, and C. Wunsch, 2015: ECCO version 4: an integrated framework for non-linear inverse modeling and global ocean state estimation. Geoscientific Model Development, 8, 3071-3104, http://dx.doi.org/10.5194/gmd-8-3071-2015, URL <http://www.geosci-model-dev.net/8/3071/2015/>
+Forget, G., J.-M. Campin, P. Heimbach, C. N. Hill, R. M. Ponte, and C. Wunsch, 2015: ECCO version 4: an integrated framework for non-linear inverse modeling and global ocean state estimation. Geoscientific Model Development, 8, 3071-3104, <http://dx.doi.org/10.5194/gmd-8-3071-2015>, <http://www.geosci-model-dev.net/8/3071/2015/>
 
-Forget, G., J.-M. Campin, P. Heimbach, C. N. Hill, R. M. Ponte, and C. Wunsch, 2016: ECCO Version 4: Second Release, http://hdl.handle.net/1721.1/102062, URL <https://dspace.mit.edu/bitstream/handle/1721.1/102062/standardAnalysis.pdf?sequence=1>
+Forget, G., J.-M. Campin, P. Heimbach, C. N. Hill, R. M. Ponte, and C. Wunsch, 2016: ECCO Version 4: Second Release, <http://hdl.handle.net/1721.1/102062>, [direct download][]