Run shell scripts through shellcheck

Fix for memory leak issue in indexer.c, that surfaces on windows

odb: `git_odb_object` contents are never NULL

This is a contract that we made in the library and that we need to uphold. The
contents of a blob can never be NULL because several parts of the library (including
the filter and attributes code) expect `git_blob_rawcontent` to always return a
valid pointer.

Update message for error during push

Clarify the git_remote_ls() documentation

fetch: clear the connection data on close

travis: disable the cert callback on OSX

The sshd on OSX has stopped responding to the setting which this test
assumes is there, so let's disable it until we can figure out what's
happening.

When we fetch twice with the same remote object, we did not properly
clear the connection flags, so we would leak state from the last
connection.

This can cause the second fetch with the same remote object to fail if
using a HTTP URL where the server redirects to HTTPS, as the second
fetch would see `use_ssl` set and think the initial connection wanted to
downgrade the connection.

On disconnect we simply ask the transport to close the connection, we do
not free it.

Make it clear that this is not the ls-remote command but a way to access
the data we have and how long it's kept around.

Fix missing object in tests/resources/crlf by changing the tail commit

Provide a convenience function `git_remote_push()`

Fixed active_refspecs field not initialized on new git_remote objects

push: use the common refspec parser

Fixed a couple Clang warnings

When attempting to update a reference on a remote during push, and the
reference on the remote refers to a commit that does not exist locally,
then we should report a more clear error message.

When creating a new remote, contrary to loading one from disk,
active_refspecs was not populated. This means that if using the new
remote to push, git_push_update_tips() will be a no-op since it
checks the refspecs passed during the push against the base ones
i.e. active_refspecs. And therefore the local refs won't be created
or updated after the push operation.

Fixed git2.h not including threads.h anymore

Fix typo in THREADING.md

There is one well-known and well-tested parser which we should use,
instead of implementing parsing a second time.

The common parser is also augmented to copy the LHS into the RHS if the
latter is empty.

The expressions test had to change a bit, as we now catch a bad RHS of a
refspec locally.

Add test information to contributing guidelines

Rename git_threads_ to git_libgit2_

If the user does not pass any refspecs to push, try to use those
configured via the configuration or via add_push().

We have the step-by-step method in the initialization function as we
want to remove references based on the list of references which are
already there, and we can use the convenience function for testing the
main push.

This function, similar in style to git_remote_fetch(), performs all the
steps required for a push, with a similar interface.

The remote callbacks struct has learnt about the push callbacks, letting
us set the callbacks a single time instead of setting some in the remote
and some in the push operation.

This describes their purpose better, as we now initialize ssl and some
other global stuff in there. Calling the init function is not something
which has been optional for a while now.

Fixed GIT_REMOTE_DOWNLOAD_TAGS_ALL to behave like git 1.9.0+