Update documentation for API changes

Fixed unused warning in tests/rebase/merge.c

Do not call regfree() on an empty regex that is not successfully created...

(also removed an unused member "has_regex" from all_iter)

Fix wrong format string in git_reflog_drop() error message

Validate configuration keys

Use SecureTransport on OS X

On close, we might get a return code which looks like an error but just
means that the other side closed gracefully. Handle that.

Anything SSL is deprecated. Let's make sure we don't try to use SSL v3
when talking to the server.

Do not automatically fail on a bad certificate, but let the caller
decide. This means we don't need our switch on errors anymore but can
return a string representation from the security framework.

This is what it's meant all along, but now we actually have multiple
implementations, it's clearer to use the name of the library.

Instead, provide git_tls_stream_new() to ask for the most appropriate
encrypted stream and use it in our HTTP transport.

As an alternative to OpenSSL when we're on OS X. This one can actually
take advantage of stacking the streams.

config_write -- handle duplicate section headers when deleting entries

Closes #2966.

Fix git_checkout_tree() to do index filemodes correctly on Windows.

Fix for Issue #3023 tests fail with no network

Moved offending tests from network to online so they will get skipped
when there is a lack of network connectivity:
-test_online_remotes__single_branch
-test_online_remotes__restricted_refspecs

Attempt to fix Windows TLS memory leak.

If git_config_delete is to work properly in the presence of duplicate section
headers, it cannot stop searching at the end of the first matching section, as
there may be another matching section later.
When config_write is used for deletion (value = NULL), it may only terminate
when the desired key is found or there are no sections left to parse.

Instead of using a config file in resources, include the config file content to
be tested directly in the test.

Add a unittest to validate bug #3043, where a duplicate empty config header
could cause deletion of a config entry to fail silently. The bug is currently
unresolved and this test will fail.

Rebase fixes

Handle invalid multiline configuration

The idea...sometimes, a filemode is user-specified via an
explicit git_index_entry.  In this case, believe the user, always.

Sometimes, it is instead built up by statting the file system.  In
those cases, go with the existing logic we have to determine
whether the file system supports all filemodes and symlinks, and
make the best guess.

On file systems which have full filemode and symlink support, this
commit should make no difference.  On others (most notably Windows),
this will fix problems things like:
* git_index_add and git_index_add_frombuffer() should be believed.
* As a consequence, git_checkout_tree should make the filemodes in
the index match the ones in the tree.
* And diffs with GIT_DIFF_UPDATE_INDEX don't write the wrong filemodes.
* And merges, and probably other downstream stuff now fixed, too.

This makes my previous changes to checkout.c unnecessary,
so they are now reverted.

Also, added a test for index_entry permissions from git_index_add
and git_index_add_frombuffer, both of which failed before these changes.

`git_rebase_init` and `git_rebase_open` should take a
`git_rebase_options` and use it for future rebase operations on
that `rebase` object.