Implement fix for stem-level deduplication in file handling

- Introduced a migration plan to address the deduplication issue where bare slugs were compared against full filenames, leading to undetected file-format collisions.
- Updated `name_for_inst` to return a deduplication key alongside the filename and metadata flag, ensuring callers use the bare slug for collision detection.
- Replaced disk-based seeding of `taken_names` with tree-based slugified names to maintain consistency and avoid extension mismatches.
- Refactored relevant modules including `dir.rs`, `project.rs`, and `api.rs` to utilize the new deduplication logic.
- Updated tests to validate the new deduplication behavior and ensure correct handling of file-format instances.

src/snapshot_middleware/json_model.rs

@@ -77,6 +77,11 @@ pub fn syncback_json_model<'sync>(
         // could have a performance cost.
         model.schema = old_inst.metadata().schema.clone();
         model.name = old_inst.metadata().specified_name.clone();
+    } else if snapshot.needs_meta_name {
+        // New instance whose filesystem name differs from the instance name
+        // (due to slugification or deduplication). Store the real name so it
+        // survives a round-trip through the filesystem.
+        model.name = Some(snapshot.new_inst().name.clone());
     }
 
     let serialized = match crate::json::to_vec_pretty_sorted(&model) {