chore: add diagnostic logging for manifest mount resolution

- Log REPO_PATH, SSH_PATH, EXTRA_VOLUMES, manifest mounts, and resolved
  volumes in compile_compose() to trace why mounts may be missing
- Log repo_path and generated compose content in _prepare_manifest_instance()
  to verify the full compose YAML at start time

apps/api/src/api/tool_instances.py

@@ -1430,6 +1430,18 @@ async def _prepare_manifest_instance(
 
     compose_content = compile_compose(manifest, variables)
 
+    logger.debug(
+        "_prepare_manifest_instance for %s: repo_path=%s compose_volumes=%s",
+        instance.id,
+        repo_path or "<empty>",
+        manifest.get("mounts", []),
+    )
+    logger.debug(
+        "Generated compose for %s:\n%s",
+        instance.id,
+        compose_content,
+    )
+
     # Cache
     instance.image_tag = image_tag
     instance.manifest_compiled_at = datetime.now()

apps/api/src/services/manifest_compiler.py

@@ -329,7 +329,21 @@ def compile_compose(manifest: dict, variables: dict[str, Any]) -> str:
         service["volumes"] = sort_volumes_by_specificity(volumes)
 
     compose = {"services": {"app": service}}
-    return yaml.dump(compose, default_flow_style=False)
+    result = yaml.dump(compose, default_flow_style=False)
+
+    # Debug: log mount resolution so we can diagnose missing mounts
+    import logging
+    logger = logging.getLogger(__name__)
+    logger.debug(
+        "compile_compose: REPO_PATH=%s SSH_PATH=%s EXTRA_VOLUMES=%s mounts=%s volumes=%s",
+        variables.get("REPO_PATH", "<empty>"),
+        variables.get("SSH_PATH", "<empty>"),
+        variables.get("EXTRA_VOLUMES", []),
+        manifest.get("mounts", []),
+        volumes,
+    )
+
+    return result
 
 
 def resolve_mount_source(mount: dict, variables: dict[str, Any]) -> str: