create-academic-research 0.1.15 → 0.1.16

package/dist/src/project.js

@@ -606,17 +606,18 @@ async function stageManagedFiles(root, specs, manifest, options) {
             nextManifest.files[relativePath] = stableManagedRecord(existing, managedRecordCandidateForWrittenFile(spec));
             continue;
         }
-        options.changes.push({
-            path: relativePath,
-            action: "skip",
-            reason: manifest ? "local edits detected" : "unknown legacy content"
-        });
+        if (isUnchangedSkippedManagedRecord(existing, currentChecksum, generatedChecksum)) {
+            nextManifest.files[relativePath] = existing;
+            continue;
+        }
+        const reason = skippedManagedRecordReason(existing, manifest !== undefined, currentChecksum);
+        options.changes.push({ path: relativePath, action: "skip", reason });
         nextManifest.files[relativePath] = stableManagedRecord(existing, {
             path: relativePath,
             policy: spec.policy,
             generated_checksum: generatedChecksum,
             current_checksum: currentChecksum,
-            reason: manifest ? "local edits detected" : "unknown legacy content"
+            reason
         });
     }
     return nextManifest;
@@ -696,6 +697,16 @@ function stableManagedRecord(existing, candidate) {
         return existing;
     return { ...candidate, updated_at: nowIso() };
 }
+function isUnchangedSkippedManagedRecord(record, currentChecksum, generatedChecksum) {
+    return Boolean(record?.reason &&
+        record.current_checksum === currentChecksum &&
+        record.generated_checksum === generatedChecksum);
+}
+function skippedManagedRecordReason(existing, hasManifest, currentChecksum) {
+    if (existing?.reason && existing.current_checksum === currentChecksum)
+        return existing.reason;
+    return hasManifest ? "local edits detected" : "unknown legacy content";
+}
 function managedManifestSemanticallyEqual(left, right) {
     if (left.version !== right.version)
         return false;
@@ -835,6 +846,8 @@ async function validateManagedManifestDrift(root, warnings) {
             continue;
         const checksum = checksumText(current);
         const record = manifest?.files[relativePath];
+        if (isUnchangedSkippedManagedRecord(record, checksum, checksumText(spec.content)))
+            continue;
         if (canSafelyUpdateManagedFile(record, checksum)) {
             warnings.push(`${relativePath} is not current; run npm run update -- --apply`);
         }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "create-academic-research",
-  "version": "0.1.15",
+  "version": "0.1.16",
   "description": "Scaffold agent-ready academic research repositories with SOTA, source ledgers, wiki memory, MCP setup, and project-local skills.",
   "type": "module",
   "license": "MIT",