checkout: use empty baseline when no index file exists

documentation: improve docs for `checkout_head`

When no index file exists and a baseline is not explicitly provided, use
an empty baseline instead of trying to load `HEAD`.

`git_checkout_head` is sadly misunderstood as something that can
switch branches.  It cannot.  Update the documentation to reflect this.

fetch: Fixed spurious update callback for existing tags.

Memory leak fixes

Fix invalid memory references

The thread local storage is used to hold some global state that
is dynamically allocated and should be freed upon exit. On
Windows, we clean up the C run-time right after execution of
registered shutdown callbacks and before cleaning up the TLS.

When we clean up the CRT, we also cause it to analyze for memory
leaks. As we did not free the TLS yet this will lead to false
positives.

Fix the issue by first freeing the TLS and cleaning up the CRT
only afterwards.

When removing an entry from the index by its position, we first
retrieve the position from the index's entries and then try to
remove the retrieved value from the index map with
`DELETE_IN_MAP`. When `index_remove_entry` returns `NULL` we try
to feed it into the `DELETE_IN_MAP` macro, which will
unconditionally call `idxentry_hash` and then happily dereference
the `NULL` entry pointer.

Fix the issue by not passing a `NULL` entry into `DELETE_IN_MAP`.

When we receive a packet of exactly four bytes encoding its
length as those four bytes it can be treated as an empty line.
While it is not really specified how those empty lines should be
treated, we currently ignore them and do not return an error when
trying to parse it but simply advance the data pointer.

Callers invoking `git_pkt_parse_line` are currently not prepared
to handle this case as they do not explicitly check this case.
While they could always reset the passed out-pointer to `NULL`
before calling `git_pkt_parse_line` and determine if the pointer
has been set afterwards, it makes more sense to update
`git_pkt_parse_line` to set the out-pointer to `NULL` itself when
it encounters such an empty packet. Like this it is guaranteed
that there will be no invalid memory references to free'd
pointers.

As such, the issue has been fixed such that `git_pkt_parse_line`
always sets the packet out pointer to `NULL` when an empty packet
has been received and callers check for this condition, skipping
such packets.

`git_index_read_index` fixes

When adding a new entry to an existing index via `git_index_read_index`,
be sure to remove the tree cache entry for that new path.  This will
mark all parent trees as dirty.

Test a rebase (both a merge rebase and an inmemory rebase) with a new
commit that adds files underneath a new subfolder.

Read a tree into an index, write the index, then re-open the index and
ensure that we are treesame to the original.

Update the flags to reset the path_len (to emulate `index_insert`)

Treat index entries with different modes as different, which they
are, at least for the purposes of up-to-date calculations.

Clear any error state upon each iteration.  If one of the iterations
ends (with an error of `GIT_ITEROVER`) we need to reset that error to 0,
lest we stop the whole process prematurely.

Read a tree into an index using `git_index_read_index` (by reading
a tree into a new index, then reading that index into the current
index), then write the index back out, ensuring that our new index
is treesame to the tree that we read.

Preliminary Haiku port

cleanup: unused warning

It looks like we're getting the operation and not doing anything
with it, when in fact we are asserting that it's not null.  Simply
assert that we are within the operation boundary instead of using
the `git_array_get` macro to do this for us.

Update CMakeLists.txt

typo fix

Use AppVeyor's Start-FileDownload cmdlet

test: Fix stat() test to mask out unwanted bits

Don't generate conflicts when checking out a modified submodule and the
submodule is dirty or modified in the workdir.