Revert "Make VisibleRefFilter.Filter reuse the refs passed from JGit."

This reverts commit b032a529f83892dfbdfb375c47a90d89756dd8ab. This
commit introduced an issue where tags were not replicated under certain
circumstances.

Bug: Issue 2500
Bug: Issue 1748
Change-Id: I9c902b99c7f656c7002cf3eab9e525f22a22fb85
Gracefully handle `buck audit` failure

Handle exception raised when invoking `buck audit` and exit
with an error message, instead of dumping a python Traceback.

Change-Id: I3786c4eddffa03117f4437314fc12ee68c689a85
Restrict the input of plugin_archetype_deploy.sh

Input mispelled option of plugin_archetype_deploy.sh
it starts to run. Restrict the input to avoid this error.
Add confirm before run.

Change-Id: I6fdc8b592679c45891210261a47285171b50e35f
Fix broken formatting in changes REST documentation

Change-Id: Ie17c25fb8f1f5956e79c750316b8086419406210
Merge "Revert "Make VisibleRefFilter.Filter reuse the refs passed from JGit."" into stable-2.9
Run change hooks and ref-updated events after indexing is done.

The change hooks and ref-updated events were run parallel to the
change (re)indexing. This meant that an event-stream sent events
to the clients before the change indexing was finished. If a client
queried for that change immediately after receiving the event it
happened that the response was not-found as the indexing wasn't yet
done.

Although we haven't had issues with a ref-updated event processors,
firing this event will also wait for the indexing task to finish
as we never know if a ref-updated event processor may trigger a
change query.

Change-Id: Iff17c5aeb9675f3991f938d31ef5048ef5b3b956
Merge "Run change hooks and ref-updated events after indexing is done." into stable-2.9
Mention deprecation of sortkey parameters in 2.9 release notes

Bug: Issue 2878
Change-Id: Idd16d5c932b3237cbaeeb8fc8f31e3ebcbf45034
Merge "Gracefully handle `buck audit` failure" into stable-2.9
Make `-S` an alias of `--start` in changes query REST API

The option had been added with the name `-S`.  Change the name
to `--start` with `-S` as an alias, making it consistent with the
naming in other REST APIs.

Add the option to the documentation.

Remove the documentation of `-P` and `-N`. These options only exist
to support online reindexing from clients with outdated JS, and are
deprecated. Keeping them in the documentation will potentially
cause confusion.

Bug: Issue 2878
Change-Id: I992acf4a3d1aeebb1ef40c6fed1afcb0fe26fa92
Add full names for options on list projects REST API

Change-Id: I1dd7a8b2e27b8172cd8f11c9047063070fa6e698
Add full names for options on list groups REST API

Change-Id: I6663eda2adc00c493624438a16ecbf4818e740e1
Merge branch 'stable-2.9' into stable-2.10

* stable-2.9:
  Add full names for options on list groups REST API
  Add full names for options on list projects REST API
  Make `-S` an alias of `--start` in changes query REST API
  Mention deprecation of sortkey parameters in 2.9 release notes
  Run change hooks and ref-updated events after indexing is done.
  Fix broken formatting in changes REST documentation
  Restrict the input of plugin_archetype_deploy.sh
  Gracefully handle `buck audit` failure
  Revert "Make VisibleRefFilter.Filter reuse the refs passed from JGit."

Conflicts:
	gerrit-server/src/main/java/com/google/gerrit/server/change/PutTopic.java
	gerrit-server/src/main/java/com/google/gerrit/server/git/MergeOp.java
	tools/pack_war.py

Change-Id: I89a9b42c049ec1365ef6dec53c73c7a10a41e888