Complete audit plan updates and enhance deduplication processes

- Updated the audit plan for the ambiguous paths follow-up, marking all critical fixes as completed, including dedup cleanup, added paths, and ref path finalization.
- Introduced a new `atlas-dedup.mdc` file detailing the deduplication system, including matching algorithms, suffix cleanup, and integration for duplicate-named instances.
- Enhanced the `syncback` process to ensure proper handling of ref paths and deduplication, improving metadata consistency and overall system reliability.
- Implemented attribute-scoped path fixes in the `FsSnapshot` to ensure only relevant lines are modified during ref path updates.

These changes improve the clarity and effectiveness of the audit process while enhancing the deduplication and synchronization mechanisms within the project.

.cursor/plans/audit_ambiguous_paths_followup_00831072.plan.md

@@ -4,19 +4,19 @@ overview: Production audit of the ambiguous-paths branch against origin/master.
 todos:
   - id: fix-metadata-drift
     content: "Fix 1: Update dedup cleanup rename flow to keep tree metadata/path indexes in sync"
-    status: in_progress
+    status: completed
   - id: fix-batch-removal-dedup
     content: "Fix 2: Exclude co-removed siblings from dedup cleanup sibling enumeration"
-    status: pending
+    status: completed
   - id: fix-added-paths
     content: "Fix 3: Extend added_paths in api.rs to include middleware extension and dedup suffix"
-    status: pending
+    status: completed
   - id: fix-ref-path-final
     content: "Fix 4: Complete Phase 2 of previous audit Fix 3 -- pass final_paths to collect_referents instead of global text rewrite"
-    status: pending
+    status: completed
   - id: fix-regression-tests
     content: "Fix 5: Add regression tests for Fixes 1-4"
-    status: pending
+    status: completed
 isProject: false
 ---