Merge pull request #845 from UWB-Biocomputing/LawrenceDevelopment

Update of Documentation Organization & Error Correction

Author: lscott-uw

docs/Developer/GHActions.md

@@ -12,5 +12,10 @@ The manual GitHub Pages action is a feature that came from wanting to quickly pu
 
 ## PlantUML Action plantUML.yml
 
-The plantUML action occurs anytime a plantUML file is modified or added during a pull request or a push to the master branch. These .puml files are supposed to be located in the UML folder within the Developer folder. This action starts by checking out the repository using [actions/checkout](https://github.com/actions/checkout) with a fetch depth of 0. The next step is to grab all of the .puml files that need to be turned into images. This is done by using a basic bash command to grab all .puml files which is then piped into an awk script to parse out the unnecessary files and construct an output string with all the necessary files. The output string will look like so: "file1.puml file2.puml file3.puml file4.puml\n". This output string is then confirmed by an echo command which prints out the string to the actions terminal. Next, the .png and .svg files are generated from the .puml files in the output string using [cloudbees/plantuml-github-action](https://github.com/cloudbees/plantuml-github-action). These files are placed within the diagrams folder located within the UML folder. Lastly, the local changes are committed then pushed to the remote repository using [stefanzweifel/git-auto-commit-action](https://github.com/stefanzweifel/git-auto-commit-action).
+The plantUML action occurs anytime a plantUML file is modified or added during a pull request or a push to the master branch. These .puml files are supposed to be located in the UML folder within the Developer folder. This action starts by checking out the repository using [actions/checkout](https://github.com/actions/checkout) with a fetch depth of 0. The next step is to grab all of the .puml files that need to be turned into images. This is done by using a basic bash command to grab all .puml files which is then piped into an awk script to parse out the unnecessary files and construct an output string with all the necessary files. The output string will look like so: "file1.puml file2.puml file3.puml file4.puml\n". This output string is then confirmed by an echo command which prints out the string to the actions terminal. Next, the .png and .svg files are generated from the .puml files in the output string using a fork of [holowinski/plantuml-github-action]. These files are placed within the diagrams folder located within the UML folder. Lastly, the local changes are committed then pushed to the remote repository using [stefanzweifel/git-auto-commit-action](https://github.com/stefanzweifel/git-auto-commit-action).
 
+
+[//]: # (Moving URL links to the bottom of the document for ease of updating - LS)
+[//]: # (Links to repo items which exist outside of the docs folder need an absolute link.)
+
+[holowinski/plantuml-github-action]: <https://github.com/UWB-Biocomputing/plantuml-github-action>

docs/Developer/index.md

@@ -2,7 +2,7 @@
 
 If you're developing Graphitti code, then here are your reference documents. 
 
-Writing new code? Then make sure to follow our [contributing guide](../../CONTRIBUTING.md) and  *document your code here*. 
+Writing new code? Then make sure to follow our [contributing guide] and  *document your code here*. 
 
 Reading code that isn't obvious? When you figure out how it works, then *document it here* and *document it in comments in the code.*
 
@@ -38,7 +38,7 @@ Students, use this [quickstart guide](StudentSetup.md) to help setup, use, and d
 - Doxygen
     - Documentation generated from source code
     - Doxygen provides web-based indices and hierarchical views of Graphitti's class and file structures
-    - [Visit Doxygen Generated Documentation](https://uwb-biocomputing.github.io/Graphitti/Doxygen/html/index.html)
+    - [Visit Doxygen Generated Documentation]
     - Document code in the `.h` file using the [Doxygen Style Guide](../Doxygen/DoxygenStyleGuide.md) format
     - [Doxygen Update Guide](../Doxygen/DoxygenUpdateGuide.md)
 - [Event buffering](eventBuffering.md) in vertex classes.
@@ -50,3 +50,10 @@ Students, use this [quickstart guide](StudentSetup.md) to help setup, use, and d
 
 ---------
 [<< Go back to the Graphitti home page](../index.md)
+
+[//]: # (Moving URL links to the bottom of the document for ease of updating - LS)
+[//]: # (Links to repo items which exist outside of the docs folder need an absolute link.)
+
+[contributing guide]: <https://github.com/UWB-Biocomputing/Graphitti/blob/master/CONTRIBUTING.md>
+[Visit Doxygen Generated Documentation]: <https://uwb-biocomputing.github.io/Graphitti/Doxygen/html/index.html>
+