This fixes an issue checking file modes in the tests that
initialize a repo from a template directory when a symlink is
used in the template. Also, this updates some other places where
we are examining file modes to use the new macros.
This adds some tests for updating the index and having it remove
items to make sure that the iteration over the index still works
even as earlier items are removed.
In testing with valgrind, this found a path that would use the
path string from the index entry after it had been freed. The
bug fix is simply to copy the path of the index entry before
doing any actual index manipulation.
This adds three new public APIs for manipulating the index:
1. `git_index_add_all` is similar to `git add -A` and will add
files in the working directory that match a pathspec to the
index while honoring ignores, etc.
2. `git_index_remove_all` removes files from the index that match
a pathspec.
3. `git_index_update_all` updates entries in the index based on
the current contents of the working directory, either added
the new information or removing the entry from the index.
