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.

src/syncback/fs_snapshot.rs

@@ -451,8 +451,10 @@ impl FsSnapshot {
     ///
     /// For each entry in `substitutions` (old_path → new_path), finds all
     /// `.meta.json5` and `.model.json5` files in the snapshot and replaces
-    /// occurrences of the old path with the new path. This fixes tentative
-    /// ref paths that didn't include dedup suffixes.
+    /// occurrences of the old path with the new path **only on lines that
+    /// contain a `Rojo_Ref_` key**. This prevents unrelated string values
+    /// (property values, comments, etc.) from being altered by the
+    /// substitution.
     pub fn fix_ref_paths(&mut self, substitutions: &[(String, String)]) {
         if substitutions.is_empty() {
             return;
@@ -482,18 +484,95 @@ impl FsSnapshot {
                 continue;
             }
 
-            let mut modified = text.to_string();
-            for (old_path, new_path) in substitutions {
-                if old_path == new_path {
-                    continue;
+            // Attribute-scoped replacement: only apply substitutions on
+            // lines that contain a Rojo_Ref_ key. This prevents accidental
+            // mutation of unrelated string values in the same file.
+            let mut modified_lines: Vec<String> = Vec::new();
+            let mut any_changed = false;
+            for line in text.split('\n') {
+                if line.contains("Rojo_Ref_") {
+                    let mut new_line = line.to_string();
+                    for (old_path, new_path) in substitutions {
+                        if old_path == new_path {
+                            continue;
+                        }
+                        new_line = new_line.replace(old_path.as_str(), new_path.as_str());
+                    }
+                    if new_line != line {
+                        any_changed = true;
+                    }
+                    modified_lines.push(new_line);
+                } else {
+                    modified_lines.push(line.to_string());
                 }
-                // Replace exact path matches and prefix matches (path + "/")
-                modified = modified.replace(old_path.as_str(), new_path.as_str());
             }
 
-            if modified != text {
-                *contents = modified.into_bytes();
+            if any_changed {
+                *contents = modified_lines.join("\n").into_bytes();
             }
         }
     }
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn fix_ref_paths_only_touches_ref_lines() {
+        let mut snap = FsSnapshot::new();
+
+        let meta_content = r#"{
+  "properties": {
+    "Description": "Path is Workspace/Foo"
+  },
+  "attributes": {
+    "Rojo_Ref_PrimaryPart": "Workspace/Foo"
+  }
+}"#;
+        snap.added_files.insert(
+            PathBuf::from("/test/init.meta.json5"),
+            meta_content.as_bytes().to_vec(),
+        );
+
+        let substitutions = vec![("Workspace/Foo".to_string(), "Workspace/Foo~1".to_string())];
+        snap.fix_ref_paths(&substitutions);
+
+        let result = std::str::from_utf8(snap.added_files.get(Path::new("/test/init.meta.json5")).unwrap()).unwrap();
+
+        assert!(
+            result.contains(r#""Rojo_Ref_PrimaryPart": "Workspace/Foo~1""#),
+            "Rojo_Ref line should be updated. Got:\n{}",
+            result
+        );
+        assert!(
+            result.contains(r#""Description": "Path is Workspace/Foo""#),
+            "Non-ref property line should NOT be changed. Got:\n{}",
+            result
+        );
+    }
+
+    #[test]
+    fn fix_ref_paths_ignores_non_meta_files() {
+        let mut snap = FsSnapshot::new();
+
+        snap.added_files.insert(
+            PathBuf::from("/test/script.luau"),
+            b"-- Rojo_Ref_PrimaryPart Workspace/Foo".to_vec(),
+        );
+
+        let substitutions = vec![("Workspace/Foo".to_string(), "Workspace/Foo~1".to_string())];
+        snap.fix_ref_paths(&substitutions);
+
+        let result = std::str::from_utf8(snap.added_files.get(Path::new("/test/script.luau")).unwrap()).unwrap();
+        assert!(
+            result.contains("Workspace/Foo"),
+            "Non-meta file should not be touched. Got: {}",
+            result
+        );
+        assert!(
+            !result.contains("Workspace/Foo~1"),
+            "Non-meta file should not have substitution applied"
+        );
+    }
+}