Add case.fpp, cmake/, coverage.py to ALWAYS_RUN_ALL; fix retry loop and missing binary warning

- case.fpp and toolchain/cmake/ are invisible to gcov (Fypp-inlined
  or non-Fortran) but affect all tests. coverage.py itself must
  trigger a full run to validate pruning logic changes.
- Fix commit-cache retry: pushed=true was emitted even when all 3
  push attempts failed.
- Warn when a target binary is missing during cache build so cache
  quality issues are visible.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: sbryngelson

.github/workflows/test.yml

@@ -404,12 +404,13 @@ jobs:
             git commit -m "Regenerate gcov coverage cache
 
           Automatically rebuilt because cases.py changed."
+            pushed=false
             for i in 1 2 3; do
-              git pull --rebase && git push && break
+              git pull --rebase && git push && { pushed=true; break; }
               echo "Push attempt $i failed, retrying in 5s..."
               sleep 5
             done
-            echo "pushed=true" >> "$GITHUB_OUTPUT"
+            echo "pushed=$pushed" >> "$GITHUB_OUTPUT"
           fi
 
       - name: Post PR Comment

toolchain/mfc/test/coverage.py

@@ -45,14 +45,21 @@
     "src/common/include/omp_macros.fpp",
     "src/common/include/shared_parallel_macros.fpp",
     "src/common/include/macros.fpp",
+    "src/common/include/case.fpp",
     "toolchain/mfc/test/cases.py",
     "toolchain/mfc/test/case.py",
     "toolchain/mfc/params/definitions.py",
     "toolchain/mfc/run/input.py",
     "toolchain/mfc/case_validator.py",
+    "toolchain/mfc/test/coverage.py",
     "CMakeLists.txt",
 ])
 
+# Directory prefixes: any changed file under these paths triggers full suite.
+ALWAYS_RUN_ALL_PREFIXES = (
+    "toolchain/cmake/",
+)
+
 
 def _get_gcov_version(gcov_binary: str) -> str:
     """Return the version string from gcov --version."""
@@ -304,6 +311,8 @@ def _run_single_test_direct(test_info: dict, gcda_dir: str, strip: str) -> tuple
     failures = []
     for target_name, bin_path in binaries:
         if not os.path.isfile(bin_path):
+            cons.print(f"[yellow]Warning: binary {target_name} not found "
+                       f"at {bin_path} for test {uuid}[/yellow]")
             continue
         cmd = mpi_cmd + [bin_path]
         try:
@@ -574,12 +583,16 @@ def get_changed_files(root_dir: str, compare_branch: str = "master") -> Optional
 
 def should_run_all_tests(changed_files: set) -> bool:
     """
-    Return True if any changed file is in ALWAYS_RUN_ALL.
+    Return True if any changed file is in ALWAYS_RUN_ALL or under
+    ALWAYS_RUN_ALL_PREFIXES.
 
-    GPU macro files and toolchain files cannot be correctly analyzed by CPU
-    coverage — changes to them must always trigger the full test suite.
+    GPU macro files, Fypp includes, and build system files cannot be
+    correctly analyzed by CPU coverage — changes to them must always
+    trigger the full test suite.
     """
-    return bool(changed_files & ALWAYS_RUN_ALL)
+    if changed_files & ALWAYS_RUN_ALL:
+        return True
+    return any(f.startswith(ALWAYS_RUN_ALL_PREFIXES) for f in changed_files)
 
 
 def filter_tests_by_coverage(

toolchain/mfc/test/test_coverage_unit.py

@@ -254,6 +254,26 @@ def test_cmakelists_triggers_all(self):
             {"CMakeLists.txt"}
         ) is True
 
+    def test_case_fpp_triggers_all(self):
+        assert should_run_all_tests(
+            {"src/common/include/case.fpp"}
+        ) is True
+
+    def test_coverage_py_triggers_all(self):
+        assert should_run_all_tests(
+            {"toolchain/mfc/test/coverage.py"}
+        ) is True
+
+    def test_cmake_dir_triggers_all(self):
+        assert should_run_all_tests(
+            {"toolchain/cmake/FindFFTW.cmake"}
+        ) is True
+
+    def test_cmake_subdir_triggers_all(self):
+        assert should_run_all_tests(
+            {"toolchain/cmake/some/nested/file.cmake"}
+        ) is True
+
     def test_simulation_module_does_not_trigger_all(self):
         assert should_run_all_tests(
             {"src/simulation/m_rhs.fpp"}