diff --git a/lyrashield/interface/main.py b/lyrashield/interface/main.py
index 6899cc9..9844d77 100644
--- a/lyrashield/interface/main.py
+++ b/lyrashield/interface/main.py
@@ -25,6 +25,8 @@
     get_global_report_state,
     initial_run_record,
     sanitize_attachments,
+    sanitize_local_sources,
+    sanitize_targets_info,
     validate_run_record,
 )
 from lyrashield.artifacts.writer import (
@@ -1080,12 +1082,12 @@ def _persist_run_record(
     run_record = initial_run_record(
         args.run_name,
         auth_mode=codex.auth_mode(load_settings().llm.model),
-        targets_info=args.targets_info,
+        targets_info=sanitize_targets_info(args.targets_info),
         extra={
             "scan_mode": args.scan_mode,
             "instruction": args.instruction,
             "non_interactive": args.non_interactive,
-            "local_sources": getattr(args, "local_sources", []),
+            "local_sources": sanitize_local_sources(getattr(args, "local_sources", [])),
             "attachments": sanitize_attachments(getattr(args, "attachments", [])),
             "diff_scope": getattr(args, "diff_scope", {"active": False}),
             "scope_mode": args.scope_mode,
diff --git a/lyrashield/interface/utils.py b/lyrashield/interface/utils.py
index ada826a..5e3aaee 100644
--- a/lyrashield/interface/utils.py
+++ b/lyrashield/interface/utils.py
@@ -1310,7 +1310,7 @@ def resolve_diff_scope_context(
             raise
 
     if not repo_scopes:
-        if scope_mode == "auto":
+        if scope_mode == "auto" and diff_head is None:
             metadata: dict[str, Any] = {"active": False, "mode": scope_mode}
             if skipped_non_git:
                 metadata["skipped_non_git_sources"] = skipped_non_git
@@ -1326,13 +1326,10 @@ def resolve_diff_scope_context(
     instruction_block = build_diff_scope_instruction(repo_scopes)
     total_analyzable = sum(len(scope.analyzable_files) for scope in repo_scopes)
     total_deleted = sum(len(scope.deleted_files) for scope in repo_scopes)
+    # Each changed path counts once: modified already carries copied paths and
+    # low-similarity renames, so adding renamed+copied again double-counts.
     total_changed = sum(
-        len(scope.added_files)
-        + len(scope.modified_files)
-        + len(scope.renamed_files)
-        + len(scope.copied_files)
-        + len(scope.deleted_files)
-        for scope in repo_scopes
+        len(scope.analyzable_files) + len(scope.deleted_files) for scope in repo_scopes
     )
     metadata = {
         "active": True,