diff --git a/repo b/repo
index c99abdc..6d2f647 100755
--- a/repo
+++ b/repo
@@ -566,9 +566,19 @@ ensure_syqure_submodules() {
 
   echo -e "${CYAN}→ ${repo} submodules${NC}"
   git -C "$repo" submodule sync --recursive >/dev/null 2>&1 || true
-  if ! git -C "$repo" submodule update --init --recursive --depth 1; then
-    echo -e "${YELLOW}WARN: ${repo} shallow submodule update failed; retrying full depth${NC}"
-    if ! git -C "$repo" submodule update --init --recursive; then
+  git -C "$repo" config submodule.external/llvm-project.shallow true >/dev/null 2>&1 || true
+  git -C "$repo" config submodule.external/llvm-project.partialClone true >/dev/null 2>&1 || true
+  git -C "$repo" config submodule.external/llvm-project.partialCloneFilter blob:none >/dev/null 2>&1 || true
+
+  # Keep llvm-project shallow because it is large.
+  if ! git -C "$repo" submodule update --init --depth 1 --filter=blob:none -- external/llvm-project; then
+    echo -e "${RED}✗ ${repo} llvm-project shallow submodule update failed${NC}" >&2
+    return 1
+  fi
+
+  if ! git -C "$repo" submodule update --init --recursive --depth 1 -- codon sequre; then
+    echo -e "${YELLOW}WARN: ${repo} shallow codon/sequre update failed; retrying full depth${NC}"
+    if ! git -C "$repo" submodule update --init --recursive -- codon sequre; then
       echo -e "${RED}✗ ${repo} submodule update failed${NC}" >&2
       return 1
     fi
diff --git a/src-tauri/Cargo.lock b/src-tauri/Cargo.lock
index a0d9b46..86082ed 100644
--- a/src-tauri/Cargo.lock
+++ b/src-tauri/Cargo.lock
@@ -598,7 +598,7 @@ checksum = "2af50177e190e07a26ab74f8b1efbfe2ef87da2116221318cb1c2e82baf7de06"
 
 [[package]]
 name = "biovault"
-version = "0.1.152"
+version = "0.1.154"
 dependencies = [
  "anyhow",
  "base64 0.22.1",
diff --git a/src-tauri/src/commands/runs.rs b/src-tauri/src/commands/runs.rs
index 90cd5e5..6ecf428 100644
--- a/src-tauri/src/commands/runs.rs
+++ b/src-tauri/src/commands/runs.rs
@@ -257,6 +257,7 @@ pub async fn execute_analysis(
     // Capture original environment for logging
     let original_path = env::var("PATH").unwrap_or_default();
     let original_java_home = env::var("JAVA_HOME").ok();
+    let original_java_cmd = env::var("JAVA_CMD").ok();
 
     let mut env_lines = vec![
         "=== Nextflow environment ===".to_string(),
@@ -279,6 +280,12 @@ pub async fn execute_analysis(
                 .clone()
                 .unwrap_or_else(|| "<unset>".to_string())
         ),
+        format!(
+            "  JAVA_CMD (original) = {}",
+            original_java_cmd
+                .clone()
+                .unwrap_or_else(|| "<unset>".to_string())
+        ),
     ];
 
     let config = match biovault::config::get_config() {
@@ -319,8 +326,12 @@ pub async fn execute_analysis(
     }
 
     let mut java_home_set = false;
+    let mut java_cmd_set = false;
     if let Some(java_bin) = resolve_binary_path(config.as_ref(), "java") {
         env_lines.push(format!("  java binary = {}", java_bin));
+        env::set_var("JAVA_CMD", &java_bin);
+        env_lines.push(format!("  JAVA_CMD set from java binary = {}", java_bin));
+        java_cmd_set = true;
         if let Some(java_home) = derive_java_home(&java_bin) {
             env::set_var("JAVA_HOME", &java_home);
             env_lines.push(format!(
@@ -345,6 +356,26 @@ pub async fn execute_analysis(
         }
     }
 
+    if !java_cmd_set {
+        match original_java_cmd.as_deref() {
+            Some(existing) => {
+                if std::path::Path::new(existing).exists() {
+                    env_lines.push(format!("  JAVA_CMD retained (pre-existing) = {}", existing));
+                } else {
+                    env::remove_var("JAVA_CMD");
+                    env_lines.push(format!(
+                        "  JAVA_CMD removed (pre-existing path missing) = {}",
+                        existing
+                    ));
+                }
+            }
+            None => {
+                env::remove_var("JAVA_CMD");
+                env_lines.push("  JAVA_CMD (effective) = <unset>".to_string());
+            }
+        }
+    }
+
     let nxf_home_path = biovault_home.join("data").join("nextflow");
     match fs::create_dir_all(&nxf_home_path) {
         Ok(_) => {
@@ -366,6 +397,10 @@ pub async fn execute_analysis(
         "  JAVA_HOME (effective) = {}",
         env::var("JAVA_HOME").unwrap_or_else(|_| "<unset>".to_string())
     ));
+    env_lines.push(format!(
+        "  JAVA_CMD (effective) = {}",
+        env::var("JAVA_CMD").unwrap_or_else(|_| "<unset>".to_string())
+    ));
     env_lines.push(format!(
         "  NXF_HOME (effective) = {}",
         env::var("NXF_HOME").unwrap_or_else(|_| "<unset>".to_string())