Simplify command classes and examples (#106)

* Merge commands and executors for less indirection
* Move subprocess running, temporary file management
   and common parameters to the CommandBase class
* Improve user interaction during command execution
* Simplify and merge together demo classes
* Add a simple pixel classification ImageJ macro

Co-authored-by: Dominik Kutra <k-dominik@users.noreply.github.com>

README.md

@@ -251,8 +251,9 @@ as `ImagePlus`, containing `ImageProcessors` to access the underlying data. We t
 containers everywhere which are roughly wrapped as `Dataset > ImgPlus > Img >
 RandomAccessibleInterval`.
 
-**Testing:** no real tests are included right now, but you can run the `main` method in
-`WorkflowTests.java` which fires up an ImageJ instance for each of the three plugins.
+### Demo
+
+`src/test/java/org/ilastik/ilastik4ij/Demo.java` contains usage examples of various workflows.
 
 ### Manually test in a local Fiji installation
 

examples/pixel_classification.ijm

@@ -0,0 +1,5 @@
+project = "src/test/resources/pixel_class_2d_cells_apoptotic.ilp";
+input = "2d_cells_apoptotic.tif";
+
+open(input);
+run("Run Pixel Classification Prediction", "projectfilename=" + project + " input=" + input + " pixelclassificationtype=Probabilities");