tree: handle removal of all entries in the updater

When we remove all entries in a tree, we should remove that tree from
its parent rather than include the empty tree.

Tree updater fixups

When we want to remove the file, use the basename as the name of the
entry to remove, instead of the full one, which includes the directories
we've inserted into the stack.

This gives us trees with subdirectories, which the new test needs.

Add a method specifically for modifying trees

Instead of going through the usual steps of reading a tree recursively
into an index, modifying it and writing it back out as a tree, introduce
a function to perform simple updates more efficiently.

`git_tree_create_updated` avoids reading trees which are not modified
and supports upsert and delete operations. It is not as versatile as
modifying the index, but it makes some common operations much more
efficient.

Misc fixes

Fix unused variable 'message' warning

Fix `git_commit_create` for an initial commit

`test_commit_commit__create_initial_commit_parent_not_current` was not correctly 
testing that `HEAD` was not changed. Now we grab the oid that it was pointing to
before the call to `git_commit_create` and the oid that it's pointing to afterwards
and compare those.

Rebase: rebase a branch with no merge base for in-memory

When calling `git_commit_create` with an empty array of `parents` and `parent_count == 0` 
the call will segfault at https://github.com/libgit2/libgit2/blob/master/src/commit.c#L107 
when it's trying to compare `current_id` to a null parent oid. 

This just puts in a check to stop that segfault.

When determining diffs between two iterators we may need to
recurse into an unmatched directory for the "new" iterator when
it is either a prefix to the current item of the "old" iterator
or when untracked/ignored changes are requested by the user and
the directory is untracked/ignored.

When advancing into the directory and no files are found, we will
get back `GIT_ENOTFOUND`. If so, we simply skip the directory,
handling resulting unmatched old items in the next iteration. The
other case of `iterator_advance_into` returning either
`GIT_NOERROR` or any other error but `GIT_ENOTFOUND` will be
handled by the caller, which will now either compare the first
directory entry of the "new" iterator in case of `GIT_ENOERROR`
or abort on other cases.

Improve readability of the code to make the above logic more
clear.

odb: avoid inflating the full delta to read the header

We compute offsets by executing `off |= (*delta++ << 24)` for
multiple constants, where `off` is of type `size_t` and `delta`
is of type `unsigned char`. The usual arithmetic conversions (see
ISO C89 §3.2.1.5 "Usual arithmetic conversions") kick in here,
causing us to promote both operands to `int` and then extending
the result to an `unsigned long` when OR'ing it with `off`.
The integer promotion to `int` may result in wrong size
calculations for big values.

Fix the issue by making the constants `unsigned long`, causing both
operands to be promoted to `unsigned long`.

An object's size is computed by reading the object header's size
field until the most significant bit is not set anymore. To get
the total size, we increase the shift on each iteration and add
the shifted value to the total size.

We read the current value into a variable of type `unsigned
char`, from which we then take all bits except the most
significant bit and shift the result. We will end up with a
maximum shift of 60, but this exceeds the width of the value's
type, resulting in undefined behavior.

Fix the issue by instead reading the values into a variable of
type `unsigned long`, which matches the required width. This is
equivalent to git.git, which uses an `unsigned long` as well.

When `git_repository__cvar` fails we may end up with a
`ignorecase` value of `-1`. As we subsequently check if
`ignorecase` is non-zero, we may end up reporting that data
should be removed when in fact it should not.

Err on the safer side and set `ignorecase = 0` when
`git_repository__cvar` fails.

The `merge_file__xdiff` function checks if either `ours` or
`theirs` is `NULL`. The function is to be called with existing
files, though, and in fact already unconditionally dereferences
both pointers.

Remove the unnecessary check to silence warnings.

When we read the header, we want to know the size and type of the
object. We're currently inflating the full delta in order to read the
first few bytes. This can mean hundreds of kB needlessly inflated for
large objects.

Instead use a packfile stream to read just enough so we can read the two
varints in the header and avoid inflating most of the delta.

cmake: include threading libraries in pkg-config

Include any required threading libraries in our `libgit2.pc`.

Introduce `git_signature_from_buffer`

Fix return value of openssl_read (infinite loop)

Allow users to construct a signature from the type of signature
lines that actually appear in commits.

Annotated commits: differentiate between the ref names and the description

Differentiate between the ref_name used to create an annotated_commit
(that can subsequently be used to look up the reference) and the
description that we resolved this with (which _cannot_ be looked up).

The description is used for things like reflogs (and may be a ref name,
and ID something that we revparsed to get here), while the ref name must
actually be a reference name, and is used for things like rebase to
return to the initial branch.

openssl_read should return -1 in case of error.

SSL_read returns values <= 0 in case of error.

A return value of 0 can lead to an infinite loop, so the return value
of ssl_set_error will be returned if SSL_read is not successful (analog
to openssl_write).

Test that we can properly abort a rebase when it is initialized by a
revspec.  This ensures that we do not conflate revspecs and refnames.

Remove traces of `git_blob_create_fromchunks`

Allow creating copies of `git_reference` objects.

Rebase improvements with IDs