Use numeric indices for delta filenames, document limitations

- Delta files now named 0.zst, 1.zst etc — avoids path length issues
  and ambiguous separator substitution; manifest maps index to path
- PLAN.md: document delta naming rationale
- PLAN.md: document cross-file deduplication limitation and possible
  future approaches (zstd dictionary training, content-addressing, tar stream)

lib/commands/run.js

@@ -65,16 +65,16 @@ export async function runCommand(config) {
   }
 
   const manifestChanges = [];
+  let fileIndex = 0;
 
   for (const change of changes) {
-    const deltaFilename = change.path.replaceAll('/', '__') + backend.ext;
-    const outFile = join(filesDir, deltaFilename);
-
     if (change.status === 'deleted') {
       manifestChanges.push({ path: change.path, status: 'deleted' });
       continue;
     }
 
+    const deltaFilename = `${fileIndex}${backend.ext}`;
+    const outFile = join(filesDir, deltaFilename);
     const prevFile = join(prev, change.path);
     const newFile  = join(pend, change.path);
 
@@ -97,6 +97,8 @@ export async function runCommand(config) {
       status: change.status,
       delta: join('files', deltaFilename),
     });
+
+    fileIndex++;
   }
 
   // ── Phase 5: Write manifest + atomic commit ──────────────────