`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.

Fix comment for GIT_FILEMODE_LINK

Start-FileDownload maintains current directory context and allows
specifying a request timeout, see [1].

[1] https://www.appveyor.com/docs/how-to/download-file#start-filedownload-cmdlet

Haiku and Hurd both pass extra bits in struct stat::st_mode.

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.

0120000 is symbolic link, not commit

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