Flush once per tag

Not sure this is the right thing to do (maybe there is a better way to get an ID?), but it avoids
```
IntegrityError: (psycopg2.IntegrityError) duplicate key value violates unique constraint "tag_name_key"
DETAIL:  Key (name)=(group) already exists.
 [SQL: 'INSERT INTO tag (type, parent_id, name) VALUES (%(type)s, %(parent_id)s, %(name)s) RETURNING tag.id'] [parameters: {'parent_id': None, 'type': 0, 'name': u'group'}]
galaxy.tools.execute WARNING 2018-02-06 15:22:38,808 [p:2122,w:1,m:0] [uWSGIWorker1Core1] There was a failure executing a job for tool [__TAG_FROM_FILE__] - Error executing tool: (psycopg2.IntegrityError) duplicate key value violates unique constraint "tag_name_key"
```

lib/galaxy/managers/tags.py

@@ -169,6 +169,8 @@ class TagManager(object):
         item_tag_assoc.user_tname = name
         item_tag_assoc.user_value = value
         item_tag_assoc.value = lc_value
+        # Need to flush to get an ID. We need an ID to apply multiple tags with the same tname to an object.
+        self.sa_session.flush()
         return item_tag_assoc
 
     def apply_item_tags(self, user, item, tags_str):

lib/galaxy/tools/tag_collection_from_file.xml

@@ -34,13 +34,13 @@
                     <assert_contents>
                         <has_text_matching expression="^This is a line of text.\n$" />
                     </assert_contents>
-                    <metadata name="tags" value="alias:r1,orientation:forward" />
+                    <metadata name="tags" value="alias:f,alias:r1,orientation:forward" />
                 </element>
                 <element name="reverse">
                     <assert_contents>
                         <has_text_matching expression="^This is a different line of text.\n$" />
                     </assert_contents>
-                    <metadata name="tags" value="alias:r2,orientation:reverse" />
+                    <metadata name="tags" value="alias:r,alias:r2,orientation:reverse" />
                 </element>
             </output_collection>
         </test>
@@ -63,13 +63,13 @@
                         <assert_contents>
                             <has_text_matching expression="^This is a line of text.\n$" />
                         </assert_contents>
-                        <metadata name="tags" value="alias:r1,orientation:forward" />
+                        <metadata name="tags" value="alias:f,alias:r1,orientation:forward" />
                     </element>
                     <element name="reverse">
                         <assert_contents>
                             <has_text_matching expression="^This is a different line of text.\n$" />
                         </assert_contents>
-                        <metadata name="tags" value="alias:r2,orientation:reverse" />
+                        <metadata name="tags" value="alias:r,alias:r2,orientation:reverse" />
                     </element>
                 </element>
             </output_collection>

test-data/new_tags_1.txt

@@ -1,2 +1,2 @@
-forward	orientation:forward	alias:r1
-reverse	orientation:reverse	alias:r2
+forward	orientation:forward	alias:r1	alias:f
+reverse	orientation:reverse	alias:r2	alias:r