updating links, cleanup

docs/README.md

 # Documentation: nshmp-haz
 
-***nshmp-haz*** is a USGS developed software stack that supports probabilistic seismic hazard
-(PSHA) and related analyses. It is maintained by the National Seismic Hazard Model Project
-([NSHMP](https://earthquake.usgs.gov/hazards/)) within the U.S. Geological Survey's
-([USGS](https://www.usgs.gov)) earthquake hazards program ([EHP](http://earthquake.usgs.gov)).
+***nshmp-haz*** is a U.S. Geological Survey ([USGS](https://www.usgs.gov)) developed software stack
+that supports probabilistic seismic hazard (PSHA) and related analyses. It is maintained by the
+National Seismic Hazard Model Project ([NSHMP](https://earthquake.usgs.gov/hazards/)) within the
+USGS's earthquake hazards program ([EHP](http://earthquake.usgs.gov)).
 
 *nshmp-haz* supports high performance seismic hazard calculations required to generate detailed
 maps over large areas and supports a variety of USGS web services and applications related to
@@ -31,7 +31,7 @@ to use *nshmp-haz* as well as underlying model implementation details.
 
 ## Other Pages & References
 
-* [nshmp-lib](/ghsc/nshmp/nshmp-lib): USGS hazard modeling library
+* [nshmp-lib](https://code.usgs.gov/ghsc/nshmp/nshmp-lib): USGS hazard modeling library
 * [Functional PSHA](pages/Functional-PSHA.md)
 * [Probabilistic Seismic Hazard Analysis, a Primer
   [PDF]](http://www.opensha.org/sites/opensha.org/files/PSHA_Primer_v2_0.pdf)

docs/pages/Building-&-Running.md

@@ -40,15 +40,16 @@ measures. For example:
 java -cp path/to/nshmp-haz.jar gov.usgs.earthquake.nshmp.HazardCalc model sites [config]
 ```
 
-At a minimum, the hazard source [model](hazard-model) and the [site](site-specification)(s) at
+At a minimum, the hazard source [model](Hazard-Model.md) and the [site](Site-Specification.md)(s) at
 which to perform calculations must be specified. The source model should specified a path to a
 directory. A single site may be specified with a string; multiple sites must be specified using
 either a comma-delimited (CSV) or [GeoJSON](http://geojson.org) file. The path to a custom
-[configuration](calculation-configuration) file containing user-specific settings may optionally
+[configuration](Calculation-Configuration.md) file containing user-specific settings may optionally
 be supplied as a third argument. It can be used to override any calculation settings; if absent
-[default](calculation-configuration) values are used.
+[default](Calculation-Configuration.md) values are used.
 
-See the [examples](/ghsc/nshmp/nshmp-haz-v2/-/tree/master/etc/examples) directory for more details.
+See the [examples](https://code.usgs.gov/ghsc/nshmp/nshmp-haz-v2/-/tree/master/etc/examples)
+directory for more details.
 
 ### Computing Disaggregations
 
@@ -62,7 +63,7 @@ java -cp nshmp-haz.jar gov.usgs.earthquake.nshmp.DisaggCalc model sites returnPe
 
 Disaggregations build on and output `HazardCalc` results along with other disaggregation specific
 files. Disaggregations also have some independent
-[configuration](calculation-configuration#config-disagg) options.
+[configuration](Calculation-Configuration.md#config-disagg) options.
 
 ## Run with [Docker](https://docs.docker.com/install/)
 
@@ -112,17 +113,17 @@ Where: (TODO links below need checking)
   * hazard = `HazardCalc`
   * rate = `RateCalc`
 
-* `MODEL` is the [USGS model (NSHM)](usgs-models) to run:
-  * CONUS-2018: [Conterminous U.S. 2018](https://github.com/usgs/nshm-conus)
+* `MODEL` is the [USGS model (NSHM)](USGS-Models.md) to run:
+  * CONUS-2018: [Conterminous U.S. 2018](https://code.usgs.gov/ghsc/nshmp/nshm-conus)
   * HAWAII-2021: [Hawaii 2021](https://code.usgs.gov/ghsc/nshmp/nshm-hawaii)
 
 * `RETURN_PERIOD`, in years, is only required when running a disaggregation
 
 * Other arguments:
-  * (required) The absolute path to a GeoJSON or CSV [site(s)](site-specification) file
+  * (required) The absolute path to a GeoJSON or CSV [site(s)](Site-Specification.md) file
     * CSV example: `$(pwd)/my-csv-sites.csv:/app/sites.csv`
     * GeoJSON example: `$(pwd)/my-geojson-sites.geojson:/app/sites.geojson`
-  * (optional) The absolute path to a [configuration](calculation-configuration) file
+  * (optional) The absolute path to a [configuration](Calculation-Configuration.md) file
     * Example: `$(pwd)/my-custom-config.json:/app/config.json`
   * (required) The absolute path to an output directory
     * Example: `$(pwd)/my-hazard-output:/app/output`

docs/pages/Magnitude-Frequency-Distributions.md

@@ -48,6 +48,8 @@ tree of rates for a source is also present in a model. Example:
 
 ## Tapered Gutenberg–Richter
 
+TODO: Need a new link for tapered GR MFD
+
 A [tapered Gutenberg-Richter](http://scec.ess.ucla.edu/~ykagan/moms_index.html) MFD is similar to
 Gutenberg-Richter, above, but with an exponential taper applied with a corner magnitude of `mCut`.
 The `a`-value member is optional when a logic tree of rates for a source is also present in a
@@ -98,8 +100,6 @@ example:
 }
 ```
 
-**mfd-config.json:**
-
 MFD confguration files:
 
 * mfd-map.json
@@ -255,6 +255,8 @@ Depending on the types of MFDs being modeled, a rate file may contain Gutenberg-
 or magnitude-specific rates. The branches of a rate-tree commonly have the generic ID's:
 `[R1, R2, R3, ...]` to support matching rate-trees across source-tree branches.
 
+TODO: convert example to JSON format (or see `mfd-config.json` section above)
+
 ```xml
         <!-- (optional) A magnitude uncertainty model that will be
              applied to every source: