Keep unpublished rewrites out of the empty checkpoint skip

Empty managed checkpoints skip the git commit when no allowlisted
path differs from HEAD. A staged rewrite is still unpublished on
disk at that check, so skipping would publish it in memory without
writing or committing. Only skip when nothing is staged to land.

Author: TheGreatAxios

src/session/optimized-context-store.ts

@@ -742,22 +742,25 @@ export async function createSessionStores(
         const headBefore = stagedRewrite === null ? null : await headOid(dir);
         let extraPaths: string[] = [];
 
-        const managedFilepaths = [
-          ...VENDOR_COMMIT_ROOT_FILES,
-          TOOL_OUTPUT_DIR,
-          EVIDENCE_ARCHIVE_DIR,
-          ...extraPaths,
-        ];
-        if (!(await managedPathsDiffer(dir, managedFilepaths))) {
-          const [head] = await base.log(1);
-          if (head !== undefined) {
-            pendingBlobFilepaths.clear();
-            pendingSegmentPaths.clear();
-            if (stagedRewrite !== null) {
-              liveTurnRefs = stagedRewrite;
-              unpublishedRewrite = null;
+        // Empty managed checkpoints must not create a new commit or stage
+        // session junk such as partial.jsonl. A staged unpublished rewrite
+        // is still unpublished on disk — skip would swallow the compact
+        // without writing it, so that path always goes through commit.
+        if (stagedRewrite === null) {
+          const managedFilepaths = [
+            ...VENDOR_COMMIT_ROOT_FILES,
+            TOOL_OUTPUT_DIR,
+            EVIDENCE_ARCHIVE_DIR,
+            ...pendingSegmentPaths,
+            ...pendingBlobFilepaths,
+          ];
+          if (!(await managedPathsDiffer(dir, managedFilepaths))) {
+            const [head] = await base.log(1);
+            if (head !== undefined) {
+              pendingBlobFilepaths.clear();
+              pendingSegmentPaths.clear();
+              return head;
             }
-            return head;
           }
         }