Migrate sections to use runcmd where possible.

Also fix a few typos found during review. Replace backticks code blocks by code-block directive. Update conformance tests. Ignore output.txt files.

.gitignore

@@ -12,3 +12,5 @@ _site
 
 _build/
 *.egg-info/
+
+src/_includes/cwl/**/output.txt

Makefile

@@ -28,6 +28,7 @@ watch: clean
 			--ignore='**venv' \
 			--ignore='**.github' \
 			--ignore='*.egg-info' \
+			--ignore='**_includes/**/*.txt' \
 			--watch='cwl'
 
 ## unittest-examples	:

cwl/sphinx/runcmd.py

@@ -4,6 +4,8 @@
 import subprocess
 import sys
 
+from pathlib import Path
+
 from docutils.parsers.rst import directives
 from sphinx.directives import code
 
@@ -116,7 +118,12 @@ def run(self):
         # change to that working directory before running the desired command.
         # The working directory is omitted from the final output.
         # TODO: PATCHED
-        working_directory = self.options.get('working-directory', 'src/_includes/cwl/')
+        includes_dir = Path('src/_includes/cwl/')
+        if not includes_dir.exists():
+            # You can run Sphinx from the root directory, with `make watch`
+            # for instance, or from the src directory (RTD does that).
+            includes_dir = Path('_includes/cwl')
+        working_directory = self.options.get('working-directory', includes_dir)
         if working_directory == '':
             # subprocess default value, so that we can disable it if needed.
             working_directory = None