Remove guard rails at the left to get a cleaner look.
To make it easier to determine which repositories belong to which
folder, display the repositories first, then the subfolder.

Decreased indentation a little.

Fix for #725.
Also covers #527.

This is a squashed commit of the following commits,
merging and closing pull request #1267:

commit 55fee41769
Author: Martin Spielmann <mail@martinspielmann.de>
Date:   Mon Nov 6 17:19:53 2017 +0100

    declared local variable final to fix travis build

commit 131e4d14a4
Author: Martin Spielmann <mail@martinspielmann.de>
Date:   Mon Nov 6 14:11:55 2017 +0100

    fix formatting (use tab for identation)

commit 8da5f6d596
Author: Martin Spielmann <mail@martinspielmann.de>
Date:   Mon Nov 6 13:45:39 2017 +0100

    Add repositoryListType tree. Addresses #725, 527 and includes #1224

commit 6c061651fb
Merge: f365daa3 40ee9653
Author: Martin Spielmann <mail@martinspielmann.de>
Date:   Sat Nov 4 13:19:08 2017 +0100

    Merge remote-tracking branch 'collapsible/ticket/527' into 725_nested_repos

commit f365daa3b1
Author: Martin Spielmann <mail@martinspielmann.de>
Date:   Sat Nov 4 13:10:24 2017 +0100

    first working version of tree model

When symbolic links under the base repository folder point to repositories
outside the base repository folder, the forming of relative repository
names failed and resulted in NullPointerExceptions.

Create the relative path by not following symbolic links, i.e. the link
name is taken as is and not resolved to the external path.

This also changes the whole `exactPath` method to work on Paths, instead
of Files.

Fixes #891 and fixes #837.

server.httpTimeout

setting to allow cloning big repositories over HTTP. This change fixes the java.util.concurrent.TimeoutException issue described in https://groups.google.com/d/topic/gitblit/UvDC48NpmF4/discussion .

This reverts commit 51b9b7f901.

This reverts commit c3e317a288.
Was added by mistake here. Should go into own branch to be able to merge with upstream using separate PR

if key is empty of can not be parsed, form did provide any feedback to
user before

Check if tickets need to be reindexed when the server starts. This is the
case if no ticket index exists. In that case the ticket index is built.

This is done during the start of the `ITicketService`.

For this the interface of `ITicketService` needed to change. The `start`
method was defined abstract and the specific ticket services had to
implement it. None does any real starting stuff in it.
The `start` method is now final. It calls a new abstract method `onStart`
which the specific ticket services need to implement. In the existing
implementations I just changed `start` to `onStart`.

Change from the index version of a repository index being stored in a config
file to also using index directories with the version in the name. For that,
`LuceneRepoIndexStore` is added, which adds the fixed `lucene` part to the path.
It also gives out the location of the `lucene.conf` file, which is now stored in
the index directory. This way it is automatically deleted when the directory is
deleted.

I believe that it should also provide means to store branch aliases and tips,
i.e. hide the config file completely. But this isn't implemented with this
commit, the `LuceneService` is still aware that a config file is used.

In order to be able to update the index definition, the ticket index
is assigned a version number, 2. This way the definiton can be updated
and compatability with existing index files can be checked.
The actual index is stored in a directory of name `indexVersion_codecVersion`.
This wayit is veriy easy to check if an index of a certain version exists on the
filesystem. It allows to have multiple indexes of different versions present,
so that a downgrade of the software is possible without having to reindex
again. Of coure, this is only possible if no new tickets were created since these
would be missing in the old index.

A new class `LuceneIndexStore` is introduced, which abstracts away the versioned
index directory. The idea is, that this provides one place to keep the Lucene
codec version and to allow to code compatibility rules into this class, so that
older indices can still be used if they are compatible.

In order to support sorting, Lucene 5 needs DocValue fields in an index.
So in order to make the ticket index work, i.e. show any tickets on the
tickets page, the ticket index needs to be changed, adding a DocValues
field.

The DocValuesFields are implemented for the current index, which does not
use multiple values for a field. Should at any time in the future an
existing numeric field get multiple values stored in a document, then
the index needs to know that and use SortedNumeric DocValues and SortFields
instead.

Also replace deprecated `search` method with the one without a filter
argument, since the filter isn't used anyhow.

Update the link target to the query parser syntax page of the 5.5 version.

Refactor the `LuceneSearchPage` to use an `ExternalLink` for the link
to the lucene page, so that the link target is kept and updated in the
Java code. Move the link out of the language files. This was way too
cumbersome to update the link target (which is probably why no one ever
did).

The query help text is changed to contain a variable:
`gb.queryHelp = here be some ${querySyntax} help`, which is replaced by
Wicket with a link.
The link text is a new lange file property: `gb.querySyntax`.

X-Forwarded-Host can contain port number and it is added twice in that situation
This fix just prevent adding port number if it is already there

e.g.: https://localhost:8443/rpc/?req=LIST_REPOSITORY_BRANCHES&name=repo.git

Fix #1184

Fixes the build that was broken by cherry-picking commit 2be2c2,
which resulted in an import collision on the `SecureRandom` class.

Introduce our own wrapper `SecureRandom` around `java.security.SecureRandom`.
This a) makes sure that the PRNG is seeded on creation and not when
random bytes are retrieved, and
b) uses a static instance in the `UserModel` so that lags do not occur
during operation due to potentially seeding getting blocked on Unix
when reading from the system's entropy pool. To keep the random data
still secure, the static instance will reseed all 24 hours, also a
functionality of the wrapper class.

This fixes #1063 and extends and closes PR #1116

The regular expression used for user mentions used to work
only inside sentences. Also, since it tested for whitespace, the
whitespace would get replaced, too, which would join lines together.

Instead the new regex uses boundary matchers to match against
word boundaires. As these are not capturing only the actual user
mention can be captured and is then replaced. Also, this way the
regex can ignore punctuation like in "@jim, look at this."

Since Gibtlit now requires Java 7 we can use named capture groups.
This makes the use of a centrally defined regular expression much
safer. The (admittedly only) group to capture the user name is named
"user" and can be referenced by this name. By using the name instead
of a group number, the regex could be changed without the code using
it breaking because the group number changed.

A simple test is added for user mentions, which unfortunately
has to deal with the full markdown replacement, too.

Fixes #985

So far for session cookies the secure property was only set when no
HTTP port was opened. This changes to also set it when HTTP is redirected
to the HTTPS port.

Mark the user authentication cookie to be only used for HTTP, making
it inaccessible for JavaScript engines.


If only HTTPS is used and no HTTP (i.e. also if HTTP is redirected to
HTTPS) then mark the user cookie to be sent only over secure connections.

Some public key mangers may be read-only, i.e. not allow to add or
delete keys, or to change the key comment or assigned permissions.
In such a case the respective commands should not be available on the
SSH shell and the SSH Keys panel should also not offer the possibility.

The `IPublicKeyManager` gets three new methods, modelled after the
`AuthenticationManager`:
`supportsWritingKeys`, `supportsCommentChanges` and
`supportsPermissionChanges`. They return true if a key manager allows for
keys to be written or updated.
For example the existing `FileKeyManager` will return true for all three
since it allows to store and update keys in a file.
The new `LdapKeyManager` returns false since it only accesses LDAP and
can not add or update any keys in the directory.
A future key manager might get keys from an LDAP directory but still
keep comments and permissions for it in a local copy.

If writing of keys is not supported:
* the welcome shell does not suggest adding a key,
* the `SshKeysDispatcher` does not offer the "add", "remove", "comment" and
  "permission" commands, and
* the SSH keys panel hides the "delete" button in the key list, and the
  "Add Key" form.

The hiding of the "Add key" form is not perfect since the surrounding
div is still shown, but I don't know how to hide it and it didn't look
too bad, either.

Make the SSH authentication methods used by the server configurable,
so that for example password authentication can be turned off.

For this, a `git.sshAuthenticationMethods` setting is added which is a space
separated list of authentication method names. Only the methods listed will
be enabled in the server.
This is modeled after the option of the same name from sshd_config, but it
does not offer listing multiple required methods. It leaves the door open,
though, for a later extension to support such a multi-factor authentication.

Since this also includes Kerberos authentication with GSS API, this obsoletes
the `git.sshWithKrb5` property. The latter is removed. Instead, to enable
Kerberos5 authentication, add the method name `gssapi-with-mic` to the
authentication methods list.

Add new class `LdapPublicKeyManager` which retrieves public SSH keys
from LDAP.

The attribute can be configured with the new configuration option
`realm.ldap.sshPublicKey`. The setting can be a simple attribute name,
like `sshPublicKey`, or an attribute name and a prefix for the value,
like `altSecurityIdentities:SshKey`, in which case attributes are selected
that have the name `altSecurityIdentities` and whose values start with
`SshKey:`.

Extract the inner class `LdapConnection` from the `LdapAuthProvider`
into a separate class, so that it can be used from multiple classes
that have to connect to an LDAP directory.
The new class is placed into the new package `com.gitblit.ldap`, since
it isn't specific to authentication.

The canAdmin permission is set on a LDAP user, when the user is listed
in `realm.ldap.admins` or is a member of a team listed in `realm.ldap.admins`.
This leads to inconsistent and surprising behaviour on the EditUser page
when clicking the "can admin" checkbox. Also, the "can admin" checkbox
is disabled, but not checked, for teams that are listed as admin teams.

The new behaviour implemented in this patch makes users and teams from
LDAP match local ones. That means:
* LDAP teams that are listed in `realm.ldap.admins` get the canAdmin
  property set if teams are maintained in LDAP.
* LDAP users that are listed in `realm.ldap.admins` get the canAdmin
  property set if teams are maintained in LDAP.
* LDAP users do not get the canAdmin property set, if they are only a
  member of a team listed in `realm.ldap.admins`.
* The `supportsRoleChanges` method for users and teams of the
  `LdapAuthProvider` unconditially returns false if teams are
  maintained in LDAP, not only for users and teams listed in
  `realm.ldap.admins`.
* Therefore, for all LDAP users and teams the "can admin" checkbox
  is always disabled if teams are maintained in LDAP.

Gitblit allows in its configuration to set a "manager" user (and password) which can be used
to search for the entry of a user wanting to log in. If they are both not set, an anonymous search
is attempted. In the description below, when I say "...as manager", it is either as manager or
anonymous.
So far the behaviour of Gitblit, with respect to binding to and searching in LDAP,
has been the following when a user logs in:

**bind as manager**
**search for the user**
_bind as the user_
_search for the teams_

I'll call this code flow A.

Later an additional configuration option had been added: `realm.ldap.bindpattern`.
(PR gitblit/gitblit#162) It was meant to allow for not using a manager nor anonymous binds,
by searching the directory as the user logging in.
This is done in code flow B:

**bind as manager**
_bind as user_
_search for user_
_search for teams_

Both A and B are flawed, I think. In A, it looks like a mistake to me that the binding stays with the
user after authentication. The problem that this causes is, that in LDAP server configurations
where normal users are not allowed to read groups, the team information cannot be retrieved.
I tried but failed to understand how B is supposed to work. There will always be a bind request
as either anonymous or the manager DN when the LDAP connection is created. If neither is
possible, the authentication process will fail and the user cannot log in.

When synchronizing users and teams from LDAP, the following code flow is exercised:

F:
**bind as manager**
**search for users**
**search for teams**

This patch fixes both code flows by introducing a new flow.

C:
**bind as manager**
**search for user**
_bind as user to authenticate_
**bind as manager**
**search for teams**

And it changes code flow B to the following code flow D:

_bind as user_
_search for user_
_search for teams_

With code flows A, C, D and F the following usage (and authentication) scenarios are covered.
They are described from the view of a Gitblit administrator's intent and his LDAP setup.

* Users and team should be snychronized with LDAP
	This means anonymous or a fixed account must be able to read users and groups.
	=> covered by C and F

As the above allows for authentication and is required for synchronisation, all the others below
do not cover synchronization.

* No anonymous binding allowed and no special manager binding required
	This means that users must be able to read user an group entries.
	=> covered by D

* The user DN needs to be searched, e.g. because they are not all under the same parent DN.
	This means that anonymous or a fixed account must be able to read users.
		-- anonymous or the "manager" account can also read groups
			=> covered by C
		-- anonymous or the "manager" account cannot read groups but a user can
			=> covered by A

I therefore believe that the new code will cover all common use cases. The implementation
either directly binds as the user, when `bindpattern` is not empty, or it binds anonymous or
against the manger DN to search for the user DN entry.

If it directly bound against the user DN, the user is already authenticated. It will then only check
that the user DN it found in the search is identical to the one it is currently bound against. If it
was bound against a manager DN (or anonymously) it will bind against the found user DN to
authenticate the user logging in, and will then rebind against the manager DN.

When searching for groups in LDAP, if the search fails with a result code other than SUCCESS,
the implementation will bind against the user DN, if it isn't already bound against it. It will then
repeat the search for groups under the user authorization. This is to keep backwards
compatible with the original behaviour A, in order to not break cases where the LDAP setup
would deny a manager account to search for groups but allow it for normal users.

To achieve this the implementation introduces an internal `LdapConnection` class that wraps
the connection and keeps bind state, so that a rebind as a user is possible.
This also fixes a resource leak where the connection was not closed in case that the initial bind
as the manager account did not succeed.

This commit would fix gitblit/gitblit#920