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)

PLAN.md

@@ -161,6 +161,25 @@ rsync meaningful exit codes:
 Currently basic: any non-zero exit code throws. Finer-grained handling planned as part of the
 operation abstraction refactor.
 
+## Known Limitations
+
+### Delta file naming
+Delta files are named by numeric index (e.g. `0.zst`, `1.zst`) rather than by path. The manifest
+maps each index to its source path. Path-based naming was considered but rejected because:
+- Deep directory trees can exceed filesystem filename length limits
+- Path separator substitution (e.g. `/` → `__`) is ambiguous for filenames containing that sequence
+
+### Cross-file deduplication
+Per-file deltas cannot exploit similarity between different files — each file is compressed/diffed
+in isolation. Identical or near-identical files in different locations get no benefit from each
+other. Approaches that could address this:
+- `zstd --train` to build a shared dictionary from the corpus, then compress all deltas against it
+- Content-addressed storage (deduplicate at the block or file level before delta generation)
+- Tar the entire PEND tree and delta against the previous tar (single-stream, cross-file repetition
+  is visible to the compressor — but random access for restore becomes harder)
+
+These are significant complexity increases and out of scope for now.
+
 ## Occasional Snapshots
 
 Delta chains are efficient but fragile over long chains. Periodic full snapshots (every N deltas,

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 ──────────────────