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

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.

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

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.