Deduplicate module file paths to prevent redundant scans.

Closes #6242
May also address #4053

doc/whatsnew/fragments/6242.bugfix

@@ -0,0 +1,5 @@
+Maintain and reference a set of visited files while expanding the module files
+from list of module directories, package names, and standalone files to
+prevent duplicate scans.
+
+Closes #6242

pylint/lint/pylinter.py

@@ -14,7 +14,7 @@
 import traceback
 import warnings
 from collections import defaultdict
-from collections.abc import Callable, Iterator, Sequence
+from collections.abc import Callable, Iterator, MutableSet, Sequence
 from io import TextIOWrapper
 from pathlib import Path
 from re import Pattern
@@ -878,8 +878,12 @@ def _iterate_file_descrs(
 
         The returned generator yield one item for each Python module that should be linted.
         """
+        seen_filepaths: MutableSet[str] = set()  # For deduplication of paths.
         for descr in self._expand_files(files_or_modules):
             name, filepath, is_arg = descr["name"], descr["path"], descr["isarg"]
+            if filepath in seen_filepaths:
+                continue
+            seen_filepaths.add(filepath)
             if self.should_analyze_file(name, filepath, is_argument=is_arg):
                 yield FileItem(name, filepath, descr["basename"])