Options structure for git_clone

don't walk off the end of the index

tree cache: loosen negative entry count check

While C Git has been writing entry count -1 (ie. never other negative
numbers) as invalid since day 1, it accepts all negative entry counts
as invalid. JGit follows the same rule. libgit2 should also follow, or
the index that works with C Git or JGit may someday be rejected by
libgit2.

Other reimplementations like dulwich and grit have not bothered with
parsing or writing tree cache.

ignore mkmf.log

no build artifacts
no parents

More iterator cleanup

The `git_iterator_reset` command has not been working in all cases
particularly when there is a start and end range.  This fixes it
and adds tests for it, and also extends it with the ability to
update the start/end range strings when an iterator is reset.

This removes the need to explicitly pass the repo into iterators
where the repo is implied by the other parameters.  This moves
the repo to be owned by the parent struct.  Also, this has some
iterator related updates to the internal diff API to lay the
groundwork for checkout improvements.

Add a payload param to git_cred_acquire_cb

Fixes #1128.

indexer: move the temporary buffers into the indexer object

Fix mwindow mutex initialization and error checking