Fix retry clean wiping pre-fetched deps; harden dep skip check

- Clean only source targets (not deps) in compute-node retry loops,
  so pre-fetched dependencies survive build failures on offline nodes
- Also check install dir exists (not just CMakeCache.txt) before
  skipping a dependency, guarding against configure-ok-but-build-failed

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

Author: sbryngelson

.github/workflows/frontier/bench.sh

@@ -35,8 +35,8 @@ while [ $attempt -le $max_attempts ]; do
     fi
 
     if [ $attempt -lt $max_attempts ]; then
-        echo "Build failed on attempt $attempt. Cleaning and retrying in 30s..."
-        ./mfc.sh clean
+        echo "Build failed on attempt $attempt. Cleaning source targets and retrying in 30s..."
+        ./mfc.sh clean -t pre_process simulation post_process syscheck
         sleep 30
     else
         echo "Build failed after $max_attempts attempts."

.github/workflows/frontier/test.sh

@@ -26,8 +26,8 @@ while [ $attempt -le $max_attempts ]; do
     fi
 
     if [ $attempt -lt $max_attempts ]; then
-        echo "Build failed on attempt $attempt. Cleaning and retrying in 30s..."
-        ./mfc.sh clean
+        echo "Build failed on attempt $attempt. Cleaning source targets and retrying in 30s..."
+        ./mfc.sh clean -t pre_process simulation post_process syscheck
         sleep 30
     else
         echo "Build failed after $max_attempts attempts."

.github/workflows/frontier_amd/bench.sh

@@ -35,8 +35,8 @@ while [ $attempt -le $max_attempts ]; do
     fi
 
     if [ $attempt -lt $max_attempts ]; then
-        echo "Build failed on attempt $attempt. Cleaning and retrying in 30s..."
-        ./mfc.sh clean
+        echo "Build failed on attempt $attempt. Cleaning source targets and retrying in 30s..."
+        ./mfc.sh clean -t pre_process simulation post_process syscheck
         sleep 30
     else
         echo "Build failed after $max_attempts attempts."

.github/workflows/frontier_amd/test.sh

@@ -26,8 +26,8 @@ while [ $attempt -le $max_attempts ]; do
     fi
 
     if [ $attempt -lt $max_attempts ]; then
-        echo "Build failed on attempt $attempt. Cleaning and retrying in 30s..."
-        ./mfc.sh clean
+        echo "Build failed on attempt $attempt. Cleaning source targets and retrying in 30s..."
+        ./mfc.sh clean -t pre_process simulation post_process syscheck
         sleep 30
     else
         echo "Build failed after $max_attempts attempts."

toolchain/mfc/build.py

@@ -569,7 +569,7 @@ def __build_target(target: typing.Union[MFCTarget, str], case: input.MFCInputFil
     # Dependencies are pinned to fixed versions. If already configured
     # (built & installed by a prior --deps-only step), skip entirely
     # to avoid re-entering the superbuild (which may access the network).
-    if target.isDependency and target.is_configured(case):
+    if target.isDependency and target.is_configured(case) and os.path.isdir(target.get_install_dirpath(case)):
         return
 
     for dep in target.requires.compute():