updated links in examples

etc/examples/1-hazard-curve/README.md

@@ -5,7 +5,7 @@ __Working directory:__ `/path/to/nshmp-haz/etc/examples/1-hazard-curve`
 On the command line, navigate to the directory above and execute the following:
 
 ```Shell
-hazard ../../peer/models/Set1-Case1 "Test Site, -122.0, 38.0"
+hazard ../../peer/models/Set1-Case1 site.csv
 ```
 
 The PEER models, such as that designated above, consist of simple cases for different source
@@ -15,28 +15,31 @@ testing. See the [PEER directory](../../peer/) for more information.
 The result of this calculation should be available as a single comma-delimited file containing
 several total mean hazard curves for PGA in a newly created `hazout` directory. In this example,
 the calculation configuration was derived from the model directory and the site is defined in
-file `site.csv`. See the [site specification](https://github.com/usgs/nshmp-haz/wiki/sites)
+file `site.csv`. See the [site specification](../../../docs/pages/Site-Specification.md)
 page for more details.
 
-Note that not all [calculation configuration](https://github.com/usgs/nshmp-haz/wiki/Configuration)
+Note that not all [calculation configuration](../../../docs/pages/Calculation-Configuration.md)
 parameters need be supplied; see the [configuration file](../../peer/models/Set1-Case1/config.json)
 for this example model.
 
 Also note that all output is written to a `hazout` directory by default, but the output destination
 can be specified via the
-[`output.directory`](https://github.com/usgs/nshmp-haz/wiki/configuration#config-output) parameter.
-In addition to hazard curves, the calculation configuration and a log of the calculation
-are also saved.
+[`output.directory`](../../../docs/pages/Calculation-Configuration.md#calculation-configuration-parameters)
+parameter. In addition to hazard curves, the calculation configuration and a log of the calculation
+are also saved. The primary outputs are hazard curves, hazard curves truncated below about 10⁻⁴,
+and ground motion values derived from the curves for specific return periods.
 
 __Results directory structure:__
 
 ```text
 1-hazard-curve/
   └─ hazout/
-      ├─ config.json
+      ├─ calc-config.json
       ├─ HazardCalc.log
       └─ PGA/
-          └─ curves.csv
+          ├─ curves.csv
+          ├─ curves-truncated.csv
+          └─ map.csv
 ```
 
 In the next example, we'll override the model supplied configuration with a custom file.

etc/examples/2-custom-config/README.md

@@ -13,12 +13,12 @@ In this example we've overridden the configuration supplied by the model. Specif
 * The upper end of each hazard curve has been truncated at 3 standard deviations.
 * Hazard curves have been saved as poisson probability instead of annual rate.
 * Hazard curves have been calculated for 3 `imts`
- ([intensity measures](http://usgs.github.io/nshmp-haz/javadoc/index.html?gov/usgs/earthquake/nshmp/gmm/Imt.html),
+ ([intensity measures](https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/gmm/Imt.html),
   or spectral periods).
 * The `imls` (intensity measure levels or x-values) of the resultant curves
 have been explicitely defined for each `imt`.
 
-See the [configuration specification](https://github.com/usgs/nshmp-haz/wiki/configuration)
+See the [configuration specification]../../../docs/pages/Calculation-Configuration.md)
 for details on default values and supported options and formats.
 
 __Results directory structure:__

etc/examples/3-sites-file/README.md

@@ -6,7 +6,7 @@ To compute hazard at more than one site, one may supply a comma-delimited (\*.cs
  or [GeoJSON](http://geojson.org) (\*.geojson) formatted site data file instead:
 
 ```Shell
-hazard ../../peer/models/Set1-Case1  sites.csv config.json
+hazard ../../peer/models/Set1-Case1 sites.csv config.json
 ```
 
 or
@@ -15,8 +15,8 @@ or
 hazard ../../peer/models/Set1-Case1 sites.geojson config.json
 ```
 
-The [site specification](https://github.com/usgs/nshmp-haz/wiki/sites)
-wiki page provides details on the two file formats. Note that with either format,
+The [site specification](../../../docs/pages/Site-Specification.md)
+page provides details on the two file formats. Note that with either format,
 if the name of a site is supplied, it will be included in the first column of any output curve files.
 
 __Results directory structure:__

etc/examples/5-complex-model/README.md

@@ -39,7 +39,7 @@ hazard ../../../../nshm-conus map.geojson config-map.json
 ```
 
 This computes 121 curves over a 2° by 2° area and will give you a sense of how long a larger map
-might take. This small coarse map may take 10 minutes to complete. Note that in the above two
+might take. This small, coarse map may take 10 minutes to complete. Note that in the above two
 examples we specified different output directories in the config files for each calculation.
 
 __Results directory structure:__

etc/examples/6-enhanced-output/README.md

@@ -15,14 +15,15 @@ The config file for this example, `config.json`, specified `GMM` and `SOURCE` as
 [output data types][output_types]. Note that the output curves directory now contains additional
 directories of curves by source type and GMM.
 
-[output_types]: ../../../docs/pages/Calculation-Configuration.md#calculation-configuration
+[output_types]: ../../../docs/pages/Calculation-Configuration.md#calculation-configuration-parameters
 
-See the `nshmp-haz` wiki and javadocs for more information on source types ([Wiki][source_wiki],
-[JavaDoc][source_javadoc]) and GMMs ([Wiki][gmm_wiki], [JavaDoc][gmm_javadoc]).
+See the `nshmp-haz` documentation and javadocs for more information on source types
+([docs][source_docs], [JavaDoc][source_javadoc]) and GMMs
+([docs][gmm_docs], [JavaDoc][gmm_javadoc]).
 
-[source_wiki]: ../../../docs/pages/Source-Types.md
+[source_docs]: ../../../docs/pages/Source-Types.md
 [source_javadoc]: https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/model/SourceType.html
-[gmm_wiki]: ./../../docs/pages/Ground-Motion-Models.md
+[gmm_docs]: ./../../docs/pages/Ground-Motion-Models.md
 [gmm_javadoc]: https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/gmm/package-summary.html
 
 __Results directory structure:__