changed implementation of --include-files option in collect to include files that match at least one include rule instead of all rules

the include rules are only applied to files, not directories because it is difficult to write regex strings to match both, files and all intermediate directories

ext/std/tools/collect.py

@@ -97,12 +97,19 @@ class Plugin(mpp.api.Plugin, mpp.api.Parent, mpp.api.IConfigurable, mpp.api.IRun
         self.exclude_files.append(file_path)
 
     def is_file_excluded(self, file_name):
-        for each in self.include_rules:
-            if re.match(each, os.path.basename(file_name)) == None:
+        # only apply the include rules to files - skip directories
+        if os.path.isfile(file_name):
+            for each in self.include_rules:
+                if re.match(each, os.path.basename(file_name)) != None:
+                    break;
+            # file is excluded if no include rule matches
+            else:
                 return True
+        # check exclude rules for both, files and directories
         for each in self.exclude_rules:
             if re.match(each, os.path.basename(file_name)) != None:
                 return True
+        # finally check if a file is excluded directly
         for each in self.exclude_files:
             if os.path.basename(each) == os.path.basename(file_name):
                 if os.stat(each) == os.stat(file_name):
@@ -180,7 +187,3 @@ class DirectoryReader():
             total_errors = run_per_file(plugin, os.path.basename(directory), directory)
         total_errors = total_errors # used, warnings are per file if not zero
         return 0 # ignore errors, collection is successful anyway
-    
-
-
-