Add related cwltool PR to CI

Author: GlassOfWhiskey

.github/workflows/cwltool.yml

@@ -21,10 +21,10 @@ jobs:
 
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.9.x'
+          python-version: '3.10.x'
 
       - name: Setup prerequirements
-        run: pip install "cwltest>=2.3" pytest-xdist "cwltool>=3.1.20240909164951"
+        run: pip install "cwltest>=2.3" pytest-xdist git+https://github.com/common-workflow-language/cwltool.git@refs/pull/2177/head
 
       - name: Copy in cwltool-specific configuration for the cwltest pytest plugin
         run: cp "$(python -c 'from cwltool.tests.util import get_data; print(get_data("tests/cwl-conformance/cwltool-conftest.py"))')" conftest.py

CommandLineTool.yml

@@ -51,6 +51,11 @@ $graph:
 
       ## Changelog for v1.3.0-dev1
 
+      * If an output name is present in the "cwl.output.json" file, but has
+        not been declared in the `outputs` section, it must be ignored and
+        not propagated to the next steps. Previous versions of CWL exhibited
+        undefined behaviour for this occurrence.
+
       See also the [CWL Workflow Description, v1.3.0-dev1 changelog](Workflow.html#Changelog).
       For other changes since CWL v1.0, see the
       [CWL Command Line Tool Description, v1.1 changelog](https://www.commonwl.org/v1.1/CommandLineTool.html#Changelog)

invocation.md

@@ -159,7 +159,10 @@ The exit code of the process is available to expressions in
 If the output directory contains a file named "cwl.output.json", that
 file must be loaded and used as the output object.  In this case, the
 output object should still be type-checked against the `outputs`
-section, but `outputBinding` is ignored.
+section, but `outputBinding` is ignored. If an output name is present
+in the "cwl.output.json" file, but has not been declared in the
+`outputs` section, it must be ignored and not propagated to the next
+steps.
 
 For Files and Directories, if the value of `path` is a relative path
 pattern (does not begin with a slash '/') then it is resolved relative