updated links, replaced ajk/doc_update with master. (#96)

INSTALL.md

@@ -10,7 +10,7 @@ mkdir build && cd build
 ```
 
 **Notes:**
- - Before running the following examples, it is recommended to run the unittests [tests](https://github.com/NOAA-OWP/cfe/tree/ajk/doc_update/test).
+ - Before running the following examples, it is recommended to run the unittests [tests](https://github.com/NOAA-OWP/cfe/tree/master/test).
  - All build commands are run within the `build` directory, and run commands are executed from the cfe directory.
 
 ## Example 1 (standalone mode)
@@ -22,7 +22,7 @@ make && cd ..
 ```
 ### Run
 <pre>
-Run: <a href="https://github.com/NOAA-OWP/cfe/blob/ajk/doc_update/run_cfe.sh">./run_cfe.sh</a> BASE   
+Run: <a href="https://github.com/NOAA-OWP/cfe/blob/master/run_cfe.sh">./run_cfe.sh</a> BASE   
 </pre>
 
 ## Example 2 (pseudo framework mode)
@@ -34,7 +34,7 @@ make && cd ..
 ```
 ### Run
 <pre>
-Run: <a href="https://github.com/NOAA-OWP/cfe/blob/ajk/doc_update/run_cfe.sh">./run_cfe.sh</a> FORCING
+Run: <a href="https://github.com/NOAA-OWP/cfe/blob/master/run_cfe.sh">./run_cfe.sh</a> FORCING
 </pre>
 
 ## Example 3 (pseudo framework mode)
@@ -46,7 +46,7 @@ make && cd ..
 ```
 ### Run
 <pre>
-Run: <a href="https://github.com/NOAA-OWP/cfe/blob/ajk/doc_update/run_cfe.sh">./run_cfe.sh</a> FORCINGPET
+Run: <a href="https://github.com/NOAA-OWP/cfe/blob/master/run_cfe.sh">./run_cfe.sh</a> FORCINGPET
 </pre>
 
 ## Example 4 (pseudo framework mode)
@@ -63,7 +63,7 @@ make && cd ..
 ```
 ### Run
 <pre>
-Run: <a href="https://github.com/NOAA-OWP/cfe/blob/ajk/doc_update/run_cfe.sh">./run_cfe.sh</a> AETROOTZONE
+Run: <a href="https://github.com/NOAA-OWP/cfe/blob/master/run_cfe.sh">./run_cfe.sh</a> AETROOTZONE
 </pre>
 
 ## Example 5 (nextgen framework mode)
@@ -130,7 +130,7 @@ CFE can remove mass from the modeled system through evapotranspiration (directly
 2. To run this executable you must pass the path to the corresponding configuration files for CFE, PET and AORC (in that order):  `./cfe_forcingpet ./configs/cat_89_bmi_config_cfe_pass.txt ./configs/cat_89_bmi_config_aorc.txt ./configs/cat_89_bmi_config_pet_pass.txt`
 
 ### Example 4.
-CFE rootzone-based example couples C and C++ modules and should be built with cmake, follow the instructions [here](https://github.com/NOAA-OWP/cfe/blob/ajk/doc_update/INSTALL.md#example-4-pseudo-framework-mode).
+CFE rootzone-based example couples C and C++ modules and should be built with cmake, follow the instructions [here](https://github.com/NOAA-OWP/cfe/blob/master/INSTALL.md#example-4-pseudo-framework-mode).
 
 ### NOTES:
  - The configuration files must be passed in this order: (1) the CFE configuration file, (2) the forcing configuration file, (3) the potential evapotranspiration (PET) configuration file, and (4) the soil moisture profile configuration file

README.md

@@ -1,19 +1,19 @@
 # Conceptual Functional Equivalent (CFE) Model
 
-CFE (Conceptual Functional Equivalent) is a simplified conceptual model written by Fred Ogden that is designed to be functionally equivalent to the National Water Model. To see the original author code, which is not BMI compatible, please refer to the [original_author_code](https://github.com/NOAA-OWP/cfe/tree/ajk/doc_update/original_author_code) directory.  For more information on the hypotheses and ideas underpinning the CFE model, see the [T-shirt Approximation of the National Water Model versions 1.2, 2.0, and 2.1](https://github.com/NOAA-OWP/cfe/blob/ajk/doc_update/MODEL.md) section of this document.  The remainder of this document discusses the BMI enabled and expanded CFE model. 
+CFE (Conceptual Functional Equivalent) is a simplified conceptual model written by Fred Ogden that is designed to be functionally equivalent to the National Water Model. To see the original author code, which is not BMI compatible, please refer to the [original_author_code](https://github.com/NOAA-OWP/cfe/tree/master/original_author_code) directory.  For more information on the hypotheses and ideas underpinning the CFE model, see the [T-shirt Approximation of the National Water Model versions 1.2, 2.0, and 2.1](https://github.com/NOAA-OWP/cfe/blob/master/MODEL.md) section of this document.  The remainder of this document discusses the BMI enabled and expanded CFE model. 
 
 ## Build and Run Instructions
-Detailed instructions on how to build and run CFE can be found in the [INSTALL](https://github.com/NOAA-OWP/cfe/blob/ajk/doc_update/INSTALL.md) guide.
+Detailed instructions on how to build and run CFE can be found in the [INSTALL](https://github.com/NOAA-OWP/cfe/blob/master/INSTALL.md) guide.
  - Test examples highlights
-   - Unittest (see [tests](https://github.com/NOAA-OWP/cfe/blob/ajk/doc_update/test/README.md))
+   - Unittest (see [tests](https://github.com/NOAA-OWP/cfe/blob/master/test/README.md))
    - Example 1 (standalone mode): CFE reads local forcing data
    - Example 2 (pseudo framework mode): CFE coupled to AORC (AORC provides forcing data through BMI)
    - Example 3 (pseudo framework mode): CFE coupled to AORC (provides forcing data through BMI) and PET (provides potential evapotranspiration via BMI)
    - Example 4 (pseudo framework mode): Example #3 repeated with rootzone-based actual evapotranspiration
    - Example 5 (nextgen framework mode): CFE coupled to PET module
 
 ## Model Configuration File
-A detailed description of the parameters for model configuration is provided [here](https://github.com/NOAA-OWP/cfe/tree/ajk/doc_update/configs/README.md).
+A detailed description of the parameters for model configuration is provided [here](https://github.com/NOAA-OWP/cfe/tree/master/configs/README.md).
 
 ## Getting help
 For questions, please contact XYZ, the main maintainer of the repository.
@@ -22,4 +22,4 @@ For questions, please contact XYZ, the main maintainer of the repository.
 We are constantly looking to improve the model and/or fix bugs as they arise. Please see the Git Issues for known issues or if you want to suggest adding a capability or to report a bug, please open an issue.
 
 ## Getting involved
-See general instructions to contribute to the model development ([instructions](https://github.com/NOAA-OWP/cfe/blob/ajk/doc_update/CONTRIBUTING.md)) or simply fork the repository and submit a pull request.
+See general instructions to contribute to the model development ([instructions](https://github.com/NOAA-OWP/cfe/blob/master/CONTRIBUTING.md)) or simply fork the repository and submit a pull request.

configs/README.md

@@ -1,5 +1,5 @@
 ## Configuration File
-Example configuration files are provided in this directory. To build and run the given examples see the instructions [here](https://github.com/NOAA-OWP/cfe/blob/ajk/doc_update/INSTALL.md). A detailed description of the parameters for model configuration (i.e., initialize/setup) is provided below. The asterisk (*) denotes calibratable parameters.
+Example configuration files are provided in this directory. To build and run the given examples see the instructions [here](https://github.com/NOAA-OWP/cfe/blob/master/INSTALL.md). A detailed description of the parameters for model configuration (i.e., initialize/setup) is provided below. The asterisk (*) denotes calibratable parameters.
 
 | Variable | Datatype |  Limits  | Units | Role | Process | Description |
 | -------- | -------- | ------ | ----- | ---- | ------- | ----------- |