Start of user manual, and some more README fixes

Author: mlwymore

README.md

@@ -49,19 +49,19 @@ This tool is implemented as a Flask (Python) web application. It is currently pr
 
 1. Install Julia dependencies.
 
-    `~/AppData/Local/Programs/Julia-1.9.0/bin/julia.exe -e 'using Pkg; Pkg.add(url="https://github.com/spine-tools/SpineInterface.jl.git")'`
+    `~/AppData/Local/julias/bin/julia.cmd -e 'using Pkg; Pkg.add(url="https://github.com/spine-tools/SpineInterface.jl.git")'`
 
-    `~/AppData/Local/Programs/Julia-1.9.0/bin/julia.exe -e 'using Pkg; Pkg.add(url="https://github.com/spine-tools/SpineOpt.jl.git")'`
+    `~/AppData/Local/julias/bin/julia.cmd -e 'using Pkg; Pkg.add(url="https://github.com/spine-tools/SpineOpt.jl.git")'`
 
-    `~/AppData/Local/Programs/Julia-1.9.0/bin/julia.exe -e 'using Pkg; Pkg.add(["XLSX", "DataFrames", "Distributions", "CSV", "Revise", "Cbc", "Clp"])'`
+    `~/AppData/Local/julias/bin/julia.cmd -e 'using Pkg; Pkg.add(["XLSX", "DataFrames", "Distributions", "CSV", "Revise", "Cbc", "Clp"])'`
 
 1. Run Spine Toolbox to initialize configuration. You can close it after it opens.
 
-    `python -m toolbox &`
+    `python -m spinetoolbox &`
 
 1. Configure Spine Toolbox's Julia paths.
 
-    `python venv/src/spinetoolbox/bin/configure_julia.py "C:/Users/$(whoami)/AppData/Local/Programs/Julia-1.9.0/bin/julia.exe" ""`
+    `python venv/src/spinetoolbox/bin/configure_julia.py "C:/Users/$(whoami)/AppData/Local/julias/bin/julia.cmd" ""`
 
 1. Create `config/local.json` and override default config settings as needed. At a minimum, override `"app_secret_key"` with a random string.
 

docs/user_manual/img/spine_toolbox_01.png

@@ -0,0 +1,25 @@
+# ResDEEDS User Manual
+
+## Troubleshooting
+### Spine Toolbox Workflow
+Errors in the Spine Toolbox workflow may not be directly visible in the application or console output. To troubleshoot issues with the Spine workflow, try opening Spine Toolbox by invoking the Python module directly:
+
+    python -m spinetoolbox &
+
+This will open the Spine Toolbox window:
+
+![Spine Toolbox window](img/spine_toolbox_01.png)
+
+From here, select File->Open project. In the file picker, select `ResDEEDS/spine/projects/<PROJECT>`, where PROJECT is some project that you have created in the ResDEEDS web interface.
+
+![Spine project file picker](img/spine_toolbox_02.png)
+
+With the project open, you either run the whole workflow and see where it stops, or you can select and run just part of the workflow. For example, if you suspected there was an issue with the `apply_hazards` step, you could select that step and then click the Run Selection button:
+
+![Running part of the Toolbox workflow](img/spine_toolbox_03.png)
+
+After running all or part of the workflow, you can view the console output of a particular step by selecting it in the GUI. For example, you can see the Julia output of the `apply_hazards` step by selecting it:
+
+![Viewing output of a Toolbox step](img/spine_toolbox_04.png)
+
+This allows you to debug issues with the Spine Toolbox workflow.