Correct a stale reference to GIT_EBAREINDEX

Per @carlosmn, git_index_add is now named git_index_add_bypath.

Skip untracked contained repo contents even with gitlink files

When doing a diff for use in status, we should never show the
content of a git repository contained inside another one.  The
logic to do this was looking for a .git directory and so when a
gitlink plain .git file was used, it was failing to exclude the
directory content.

In-memory packing backend

Fix submodule sort order during iteration

Add CFLAGS -Wdeclaration-after-statement

This warns local variables declarations after statement, which helps not to break MSVC

Use git_object_short_id in examples

Rename in-memory remote to anonymous and swap url and fetch order

The order in this function is the opposite to what
create_with_fetchspec() has, so change this one, as url-then-refspec is
what git does.

As we need to break compilation and the swap doesn't do that, let's take
this opportunity to rename in-memory remotes to anonymous as that's
really what sets them apart.

Fix git_odb_short_id and git_odb_exists_prefix bugs

With the changes to how git_path_dirload_with_stat handles things
that look like submodules, submodules could end up sorted in the
wrong order with the workdir iterator.  This moves the submodule
check earlier in the iterator processing of a new directory so
that the submodule name updates will happen immediately and the
sort order will be correct.

Const up members of git_merge_file_result

Introduce git_merge_head_id

Don't reset need_pack

While looping over multiple heads, an up-to-date head will clobber the `remote->need_pack` setting, preventing the rest of the machinery from building and downloading a pack-file, breaking fetches.

Update clar to 4b75388

RFC: Sandbox HOME during test execution

Fix use-after-free in submodule reload code and other memory leaks

If the first call to release a no-longer-existent submodule freed
the object, the check if a second is needed would dereference the
data that was just freed.

Fix segfault if gitmodules is invalid

When a submodule was inserted with a different path and name, the
return value from khash greater than zero was allowed to propagate
back out to the caller when it should really be zeroed.  This led
to a possible crash when reloading submodules if that was the
first time that submodule data was loaded.

The reload_all call could end up dereferencing a NULL pointer if
there was an error while attempting to load the submodules config
data (i.e. invalid content in the gitmodules file).  This fixes it.

Cleanup some warnings and mem leaks