Handle RepositoryNotFoundException when running reindex

If jgit is not able to open the repository, RepositoryNotFoundException
is raised and results in a stack trace being shown in the output of the
reindex command.

Catch the exception and print a message.

Change-Id: Icfb66567c364ac12d7f1a56b603bbb9867b633cf
Performance Fix: Minimize number of advertisedHaves

While we set up hooks in ReceiveCommits to minimize the number of
advertised refs (for instance filtering out refs/changes and
refs/cache-automerge refs), their objectIds will still be added to
BaseReceivePack.advertisedHaves (JGit), leading to an unnecessarily
complex commit graph for JGit to traverse when checking for commit
connectivity in BaseReceivePack.checkConnectivity().

By filtering the refs before the objectIds are added to advertisedHaves,
lots of time can be saved when pushing to complex Gits.

Push times for one of our Gits (warm caches):

Before fix:
real	0m42.926s

After fix:
real	0m6.325s

This Git has around 90k change/ps refs.

Change-Id: I2f0a0830bd733f908f0aeaf1eaf0412dae428a16
Fixed the spelling of indefinitely.

Change-Id: I25d0df07d412508d22083e4c42761a942d367ddc
Fixed the spelling of together and very minor rewording

Change-Id: Ib4bb64d39638e81f5db222d404fa99d7b2c2e51d
Merge "Fixed the spelling of indefinitely." into stable-2.8
Merge branch 'stable-2.6' into stable-2.7

* stable-2.6:
  Performance Fix: Minimize number of advertisedHaves

Change-Id: Id19a9ef22aa7445bf8188b79d34aeb870eadb988
Merge branch 'stable-2.7' into stable-2.8

* stable-2.7:
  Performance Fix: Minimize number of advertisedHaves
fixed minor spelling and capitalization mistakes

Change-Id: Ia62684fbcf016c3a723bb886698cbc7b97174125
Merge "fixed minor spelling and capitalization mistakes" into stable-2.8
Merge "Handle RepositoryNotFoundException when running reindex" into stable-2.8
Remove deprecated approve SSH alias

Change-Id: I540c8e9f1476c17cfd64079f513de8bd48ce774d
Fixed several spelling mistakes

Change-Id: I82c0819b8ea7d58120929efefba42b135a79f42e
Update documentation of the `review` command

The documentation states that the 'CHANGEID,PATCHSET' format for
specifying a patch set is 'legacy' and planned to be removed.

However, since there are cases where it is not possible to uniquely
identify a patch set by sha1, the CHANGEID,PATCHSET format still needs
to be supported.

Remove the section stating that the 'CHANGEID,PATCHSET' format is
legacy.

Change-Id: Ie89a69c12a3e566bd5e0c47eb8a79f4b217bd6b7
Update the 2.8 release notes with recently merged changes

Change-Id: I457b62e79fbfec8b2b140f2ac3627514fb923568
SideBySide2: Save all drafts when leaving / semi-auto focus on drafts

Keep track of all unsaved drafts and save them when leaving the page.

Using CodeMirror's "redraw" event, autofocus on the editArea of a
Draftbox when scrolled into viewportMargin. This works smoothly for
the common case where a user starts typing a draft, scrolls around to
view the file, and scrolls back to continue typing. Even if the user
forgets to scroll back and accidentally pressed "u" or "a", the draft
will be saved, minimizing potential frustration.

Change-Id: Idde88aaeb01e46f85734b48caad1de7c9b2ffba3
Merge "SideBySide2: Save all drafts when leaving / semi-auto focus on drafts" into stable-2.8
Fix getting inherited values from PluginConfig

The code for constructing a Config with the parameters from the
current project plus the missing parameters from the parent projects
relies on getting all parameter names from Config#getNames(...). The
problem is that Config#getNames(...) doesn't include parameter names
which are only available in the default Config (the Config that we
provided to the constructor when creating a new Config). This may lead
to a situation where a parameter is defined on a project, but a
grandchild of it is not inheriting this parameter although it and its
parent do not have this parameter. To fix this we are now copying the
initial Config instead of creating a new Config and providing the
existing Config as default Config to it.

Change-Id: I93ed8f7f13f1bc757e59a5897f1949540c41f9ed
Fix: File comments overlap in reply pop window

It works fine with Chrome, but when it is Firefox the
file comments apear to be overlap.
Fixed by adjusting the CSS style.

Change-Id: I905650311be3e60c91a7ffdc0150191e65c7a514
Merge "Fix getting inherited values from PluginConfig" into stable-2.8