Allow packages/modules as args with files in cfg (#9834)

Currently only files can be specified on the command line if files are
specified in mypy.ini.  This looks a great deal like a bug, especially
since packages and modules cannot be specified in the configuration
file.  This commit changes the logic to only use the files from the ini
file if none of (modules/packages/files) are specified on the command
line and adds tests to verify the new behavior.

mypy/main.py

@@ -853,9 +853,9 @@ def set_strict_flags() -> None:
     if special_opts.no_executable or options.no_site_packages:
         options.python_executable = None
 
-    # Paths listed in the config file will be ignored if any paths are passed on
-    # the command line.
-    if options.files and not special_opts.files:
+    # Paths listed in the config file will be ignored if any paths, modules or packages
+    # are passed on the command line.
+    if options.files and not (special_opts.files or special_opts.packages or special_opts.modules):
         special_opts.files = options.files
 
     # Check for invalid argument combinations.

test-data/unit/cmdline.test

@@ -1248,3 +1248,37 @@ x: str = 0
 pkg/x.py:1: error: invalid syntax
 Found 1 error in 1 file (errors prevented further checking)
 == Return code: 2
+
+[case testCmdlinePackageAndFile]
+# cmd: mypy -p pkg file
+[out]
+usage: mypy [-h] [-v] [-V] [more options; see below]
+            [-m MODULE] [-p PACKAGE] [-c PROGRAM_TEXT] [files ...]
+mypy: error: May only specify one of: module/package, files, or command.
+== Return code: 2
+
+[case testCmdlinePackageAndIniFiles]
+# cmd: mypy -p pkg
+[file mypy.ini]
+\[mypy]
+files=file
+[file pkg.py]
+x = 0  # type: str
+[file file.py]
+y = 0  # type: str
+[out]
+pkg.py:1: error: Incompatible types in assignment (expression has type "int", variable has type "str")
+
+
+[case testCmdlineModuleAndIniFiles]
+# cmd: mypy -m pkg
+[file mypy.ini]
+\[mypy]
+files=file
+[file pkg.py]
+x = 0  # type: str
+[file file.py]
+y = 0  # type: str
+[out]
+pkg.py:1: error: Incompatible types in assignment (expression has type "int", variable has type "str")
+