Apply suggestions from code review

Co-authored-by: Dachary <[email protected]>

Author: cbullinger

audit-cli/README.md

@@ -59,7 +59,7 @@ audit-cli
 │   └── find-string
 ├── analyze          # Analyze RST file structures
 │   ├── includes
-│   └── references
+│   └── file-references
 └── compare          # Compare files across versions
     └── file-contents
 ```
@@ -668,9 +668,9 @@ audit-cli/
 │   │   │   ├── analyzer.go         # Include tree building
 │   │   │   ├── output.go           # Output formatting
 │   │   │   └── types.go            # Type definitions
-│   │   └── references/             # References analysis subcommand
-│   │       ├── references.go       # Command logic
-│   │       ├── references_test.go  # Tests
+│   │   └── file-references/             # File references analysis subcommand
+│   │       ├── file_references.go       # Command logic
+│   │       ├── file_references_test.go  # Tests
 │   │       ├── analyzer.go         # Reference finding logic
 │   │       ├── output.go           # Output formatting
 │   │       └── types.go            # Type definitions