reload: fix issue with reloading modules within subpackage

sopel-irl#1314 used recursion to reload nested modules. However, in Python 2 (maybe python 3 as well), this approach leads to odd behavior with callables being unloaded/reloaded twice. The loop detects my_module.my_callable and my_callable as two separate modules to reload. The first time it detects it, the rule is added to bot._callables as a string.
I combined patched dgw branch 1056-no-dupes onto 1056-fix-with-recursion, to provide a more optimal solution to issue #1056.

sopel/loader.py

@@ -167,10 +167,13 @@ def clean_callable(func, config):
         func.rule = getattr(func, 'rule', [])
         for command in getattr(func, 'commands', []):
             regexp = get_command_regexp(prefix, command)
-            func.rule.append(regexp)
+            if regexp not in func.rule:
+                # TODO: Maybe func.rule should be a set() instead?
+                func.rule.append(regexp)
         for command in getattr(func, 'nickname_commands', []):
             regexp = get_nickname_command_regexp(nick, command, alias_nicks)
-            func.rule.append(regexp)
+            if regexp not in func.rule:
+                func.rule.append(regexp)
         if hasattr(func, 'example'):
             example = func.example[0]["example"]
             example = example.replace('$nickname', nick)

sopel/modules/reload.py

@@ -48,7 +48,7 @@ def f_reload(bot, trigger):
 
         return bot.reply('done')
 
-    if (name not in sys.modules and name not in sopel.loader.enumerate_modules(bot.config)):
+    if name not in sys.modules or name not in sopel.loader.enumerate_modules(bot.config):
         return bot.reply('"%s" not loaded, try the `load` command' % name)
 
     reload_module_tree(bot, name)
@@ -66,7 +66,7 @@ def reload_module_tree(bot, name, seen=None, silent=False):
 
     old_callables = {}
     for obj_name, obj in iteritems(vars(old_module)):
-        if callable(obj):
+        if callable(obj) and '.' not in name:
             bot.unregister(obj)
         elif (type(obj) is ModuleType and
               obj.__name__.startswith(name + '.') and