update documentation

Author: ErinWeisbart

documentation/CP-plugins-documentation/_toc.yml

@@ -6,9 +6,10 @@ parts:
 - caption: Overview
   chapters:
   - file: overview
+  - file: using_plugins
   - file: supported_plugins
   - file: unsupported_plugins
-- caption: Technical Guides
-  chapters:
-  - file: Windows
-    - file: Mac
+  - file: contributing_plugins
+  - file: troubleshooting
+  - file: citing
+  - file: versions

documentation/CP-plugins-documentation/troubleshooting.md

@@ -0,0 +1,7 @@
+# Troubleshooting
+
+| Problem | Solution | 
+|---|-----|
+| After setting the CellProfiler Plugins folder, CellProfiler won't open and returns an `error: no commands supplied` in the terminal. | You have set the CellProfiler Plugins folder to the parent folder of the plugins repository (`CellProfiler-plugins`), not the folder that contains plugins (`CellProfiler-plugins/active_plugins`). In order to get it to open, remove `setup.py` from the folder. Change the CellProfiler Plugins path to the correct path and close CellProfiler. Return `setup.py` to the parent folder. |
+| No plugins are visible in the "Add Modules" panel in CellProfiler. | You have not properly set the plugins path. Go to `CellProfiler` => `Preferences` and set the path in the `CellProfiler plugins directory` to the `active_plugins` folder in the GitHub repository that you just cloned. Select `Save` at the bottom of the Preferences window. |
+| Some but not all plugins are visible in the in the "Add Modules" panel in CellProfiler. | Not-visible plugins have unmet dependencies. Follow [installation instructions](using_plugins.md) to install dependencies for plugins. |

documentation/CP-plugins-documentation/using_plugins.md

@@ -39,7 +39,7 @@ Alternatively, if you have code for plugins that are not in the CellProfiler-plu
 
 3. **Set the plugins path in CellProfiler.**  
 - Open CellProfiler. 
-- Go to `CellProfiler` => `Preferences` and set the path in the `CellProfiler plugins directory` to the GitHub repository that you just cloned (or, if you didn't clone the whole repository, whatever location you have saved your plugins into).
+- Go to `CellProfiler` => `Preferences` and set the path in the `CellProfiler plugins directory` to the `active_plugins` folder in the GitHub repository that you just cloned (or, if you didn't clone the whole repository, whatever location you have saved your plugins into).
 - Select `Save` at the bottom of the Preferences window
 - Close CellProfiler and re-open it
 
@@ -59,7 +59,7 @@ git clone https://github.com/CellProfiler/CellProfiler-plugins.git
 
 3. **Set the plugins path in CellProfiler.**  
 - Open CellProfiler. 
-- Go to `CellProfiler` => `Preferences` and set the path in the `CellProfiler plugins directory` to the GitHub repository that you just cloned.
+- Go to `CellProfiler` => `Preferences` and set the path in the `CellProfiler plugins directory` to the `active_plugins` folder in the GitHub repository that you just cloned.
 - Select `Save` at the bottom of the Preferences window
 - Close CellProfiler
 
@@ -89,7 +89,7 @@ git clone https://github.com/CellProfiler/CellProfiler-plugins.git
 
 3. **Set the plugins path in CellProfiler.**  
 - Open CellProfiler. 
-- Go to `CellProfiler` => `Preferences` and set the path in the `CellProfiler plugins directory` to the GitHub repository that you just cloned.
+- Go to `CellProfiler` => `Preferences` and set the path in the `CellProfiler plugins directory` to the `active_plugins` folder in the GitHub repository that you just cloned.
 - Select `Save` at the bottom of the Preferences window
 - Close CellProfiler