The majority of functions are named `from_something` (with an
underscore) instead of `fromsomething`.  Update the index functions for
consistency with the rest of the library.

Use the new object_type enumeration names within the codebase.

Use the new-style index names throughout our own codebase.

The new index entry structure was not being initialized to all-zeroes.
As that structure is used to add a new entry to the current index, and
the hashing algorithm of the index making use of the uninitialized flags
to calculate the state, we might miscompute the hash of the entry and
add it at the wrong position. Later lookups would then fail.

Initialize the structure with `memset` to fix the test breaking on some
platforms.

Ensure that the buffer given to `git_index_add_frombuffer` represents a
regular blob, an executable blob, or a link.  Explicitly reject commit
entries (submodules) - it makes little sense to allow users to add a
submodule from a string; there's no possible path to success.

Use legitimate (existing) object IDs in tests so that we have the
ability to turn on strict object validation when running tests.

We were missing tests for switching the case-sensitivity of an index
in-memory and then looking up entries in it.

The idea...sometimes, a filemode is user-specified via an
explicit git_index_entry.  In this case, believe the user, always.

Sometimes, it is instead built up by statting the file system.  In
those cases, go with the existing logic we have to determine
whether the file system supports all filemodes and symlinks, and
make the best guess.

On file systems which have full filemode and symlink support, this
commit should make no difference.  On others (most notably Windows),
this will fix problems things like:
* git_index_add and git_index_add_frombuffer() should be believed.
* As a consequence, git_checkout_tree should make the filemodes in
the index match the ones in the tree.
* And diffs with GIT_DIFF_UPDATE_INDEX don't write the wrong filemodes.
* And merges, and probably other downstream stuff now fixed, too.

This makes my previous changes to checkout.c unnecessary,
so they are now reverted.

Also, added a test for index_entry permissions from git_index_add
and git_index_add_frombuffer, both of which failed before these changes.