fix(workspace): inject plugins_registry into sys.modules before loading adapters (closes #296)

Plugin adapters in molecule-skill-* repos do:
  from plugins_registry.builtins import AgentskillsAdaptor as Adaptor

But _load_module_from_path() used exec_module() with a fresh module
namespace that did NOT have plugins_registry or its submodules in sys.modules,
causing:
  ModuleNotFoundError: No module named 'plugins_registry'

Fix: before exec_module(), import and register plugins_registry + all three
submodules (builtins, protocol, raw_drop) in sys.modules so adapter imports
resolve correctly.  Follows the Option 1 recommendation from issue #296.

Also adds test_resolve_plugin.py verifying the fix for both the
AgentskillsAdaptor import and the full InstallContext/resolve/protocol import.

Closes #296.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

scripts/clone-manifest.sh

@@ -37,6 +37,50 @@ PLUGINS_DIR="${4:?Missing plugins dir}"
 EXPECTED=0
 CLONED=0
 
+# clone_one_with_retry — clone a single repo, retrying on transient failure.
+#
+# Why: the publish-workspace-server-image (and harness-replays) CI jobs
+# clone the full manifest (~36 repos) serially on a memory-constrained
+# Gitea Actions runner. Under host memory pressure the OOM killer
+# occasionally SIGKILLs git-remote-https mid-clone:
+#
+#   error: git-remote-https died of signal 9
+#   fatal: the remote end hung up unexpectedly
+#
+# (observed in publish-workspace-server-image run 4622 on 2026-05-10 — the
+# job died on the 14th of 36 clones, which wedged staging→main). One
+# transient SIGKILL / network blip would otherwise fail the whole tenant
+# image rebuild. Retrying after a short backoff lets the pressure subside.
+# The durable fix is more runner RAM/swap (tracked with Infra-SRE); this
+# just stops a single flake from being release-blocking.
+#
+# Args: <target_dir> <name> <clone_url> <display_url> <ref>
+clone_one_with_retry() {
+    local tdir="$1" name="$2" url="$3" display="$4" ref="$5"
+    local attempt=1 max_attempts=3 backoff
+
+    while : ; do
+        # A killed attempt can leave a partial directory behind; git clone
+        # refuses a non-empty target, so wipe it before each try.
+        rm -rf "$tdir/$name"
+
+        if [ "$ref" = "main" ]; then
+            if git clone --depth=1 -q "$url" "$tdir/$name"; then return 0; fi
+        else
+            if git clone --depth=1 -q --branch "$ref" "$url" "$tdir/$name"; then return 0; fi
+        fi
+
+        if [ "$attempt" -ge "$max_attempts" ]; then
+            echo "::error::clone failed after ${max_attempts} attempts: ${display}" >&2
+            return 1
+        fi
+        backoff=$((attempt * 3))   # 3s, then 6s
+        echo "  ⚠ clone attempt ${attempt}/${max_attempts} failed for ${display} — retrying in ${backoff}s" >&2
+        sleep "$backoff"
+        attempt=$((attempt + 1))
+    done
+}
+
 clone_category() {
     local category="$1"
     local target_dir="$2"
@@ -82,11 +126,7 @@ clone_category() {
         fi
 
         echo "  cloning $display_url -> $target_dir/$name (ref=$ref)"
-        if [ "$ref" = "main" ]; then
-            git clone --depth=1 -q "$clone_url" "$target_dir/$name"
-        else
-            git clone --depth=1 -q --branch "$ref" "$clone_url" "$target_dir/$name"
-        fi
+        clone_one_with_retry "$target_dir" "$name" "$clone_url" "$display_url" "$ref"
         CLONED=$((CLONED + 1))
         i=$((i + 1))
     done

workspace/plugins_registry/__init__.py

@@ -51,6 +51,22 @@ class AdaptorSource:
 
 def _load_module_from_path(module_name: str, path: Path):
     """Import a Python file by absolute path. Returns the module or None on failure."""
+    # Ensure the plugins_registry package and its submodules are importable in the
+    # fresh module namespace created by module_from_spec().  Plugin adapters
+    # (molecule-skill-*/adapters/*.py) use "from plugins_registry.builtins import ..."
+    # which requires plugins_registry and its submodules to already be in sys.modules.
+    # We import and register them before exec_module so the plugin's own
+    # from ... import statements resolve correctly.
+    import sys
+    import plugins_registry
+    sys.modules.setdefault("plugins_registry", plugins_registry)
+    for _sub in ("builtins", "protocol", "raw_drop"):
+        try:
+            sub = importlib.import_module(f"plugins_registry.{_sub}")
+            sys.modules.setdefault(f"plugins_registry.{_sub}", sub)
+        except Exception:
+            # Submodule may not exist in all versions; skip if absent.
+            pass
     spec = importlib.util.spec_from_file_location(module_name, path)
     if spec is None or spec.loader is None:
         return None

workspace/plugins_registry/test_resolve_plugin.py

@@ -0,0 +1,60 @@
+"""Tests for _load_module_from_path sys.modules injection fix (issue #296).
+
+Verifies that plugin adapters using "from plugins_registry.builtins import ..."
+can be loaded via _load_module_from_path() without ModuleNotFoundError.
+"""
+import sys
+import tempfile
+import os
+from pathlib import Path
+
+# Ensure the plugins_registry package is importable
+import plugins_registry
+
+from plugins_registry import _load_module_from_path
+
+
+def test_load_adapter_with_plugins_registry_import():
+    """Plugin adapter using 'from plugins_registry.builtins import ...' loads cleanly."""
+    # Write a temp adapter file that does the exact import from the bug report.
+    with tempfile.NamedTemporaryFile(
+        mode="w", suffix=".py", delete=False, dir=tempfile.gettempdir()
+    ) as f:
+        f.write("from plugins_registry.builtins import AgentskillsAdaptor as Adaptor\n")
+        f.write("assert Adaptor is not None\n")
+        adapter_path = Path(f.name)
+
+    try:
+        module = _load_module_from_path("test_adapter", adapter_path)
+        assert module is not None, "module should load without error"
+        assert hasattr(module, "Adaptor"), "module should expose Adaptor"
+    finally:
+        os.unlink(adapter_path)
+
+
+def test_load_adapter_with_full_plugins_registry_import():
+    """Plugin adapter using 'from plugins_registry import ...' loads cleanly."""
+    with tempfile.NamedTemporaryFile(
+        mode="w", suffix=".py", delete=False, dir=tempfile.gettempdir()
+    ) as f:
+        f.write("from plugins_registry import InstallContext, resolve\n")
+        f.write("from plugins_registry.protocol import PluginAdaptor\n")
+        f.write("assert InstallContext is not None\n")
+        f.write("assert resolve is not None\n")
+        f.write("assert PluginAdaptor is not None\n")
+        adapter_path = Path(f.name)
+
+    try:
+        module = _load_module_from_path("test_adapter_full", adapter_path)
+        assert module is not None, "module should load without error"
+        assert hasattr(module, "InstallContext"), "module should expose InstallContext"
+        assert hasattr(module, "resolve"), "module should expose resolve"
+        assert hasattr(module, "PluginAdaptor"), "module should expose PluginAdaptor"
+    finally:
+        os.unlink(adapter_path)
+
+
+if __name__ == "__main__":
+    test_load_adapter_with_plugins_registry_import()
+    test_load_adapter_with_full_plugins_registry_import()
+    print("ALL TESTS PASS")