setuptools: silence package discovery warnings

Makefile

@@ -87,7 +87,7 @@ docs: FORCE
 clean: check-python3 FORCE
 	rm -f ${MODULE}/*.pyc tests/*.pyc *.so ${MODULE}/*.so cwltool/cwlprov/*.so
 	rm -Rf ${MODULE}/__pycache__/
-	python setup.py clean --all || true
+	rm -Rf build
 	rm -Rf .coverage
 	rm -f diff-cover.html
 

setup.py

@@ -95,7 +95,29 @@
     ext_modules=ext_modules,
     # platforms='',  # empty as is conveyed by the classifier below
     # license='',  # empty as is conveyed by the classifier below
-    packages=["cwltool", "cwltool.tests", "cwltool.cwlprov"],
+    packages=[
+        "cwltool",
+        "cwltool.cwlprov",
+        "cwltool.jshint",
+        "cwltool.rdfqueries",
+        "cwltool.schemas",
+        "cwltool.tests",
+        "cwltool.tests.checker_wf",
+        "cwltool.tests.input_deps",
+        "cwltool.tests.loop",
+        "cwltool.tests.override",
+        "cwltool.tests.reloc",
+        "cwltool.tests.subgraph",
+        "cwltool.tests.test_deps_env",
+        "cwltool.tests.test_deps_env.modulefiles",
+        "cwltool.tests.tmp1.tmp2.tmp3",
+        "cwltool.tests.tmp4.alpha",
+        "cwltool.tests.trs",
+        "cwltool.tests.wf",
+        "cwltool.tests.wf.generator",
+        "cwltool.tests.wf.indir",
+        "cwltool.tests.wf.operation",
+    ],
     package_dir={"cwltool.tests": "tests"},
     include_package_data=True,
     install_requires=[