Handle dotfiles as the repo template dir and inside the template dir

Include dotfiles when copying template directory, which will handle
both a template directory itself that begins with a dotfile, and
any dotfiles inside the directory.

Ensure that we can handle template directories that begin with a
leading dot.

Ensure that `git_repository_init` honors the `init.templatedir`
configuration setting.

Update README URLs based on HTTP redirects

Fix a couple function signatures

Fixed minor typo in README.md.

typos in comments

commit: Fix memory leak in test suite

Index fill: Small fixups

fix git_blob_create_fromchunks documentation

Note that we're not checking whether the resize succeeds; in OOM cases,
we let it run with a "small" vector and hash table and see if by chance
we can grow it dynamically as we insert the new entries. Nothing to
lose really.

merge: Use `git_index__fill` to populate the index

Instead of calling `git_index_add` in a loop, use the new
`git_index_fill` internal API to fill the index with the initial staged
entries.

The new `fill` helper assumes that all the entries will be unique and
valid, so it can append them at the end of the entries vector and only
sort it once at the end. It performs no validation checks.

This prevents the quadratic behavior caused by having to sort the
entries list once after every insertion.

putting `0.` at the start of the line turns it into a numbered list.

Treat GIT_PASSTHROUGH as though git_cred_acquire_cb isn't set.

Line count overflow in git_blame_hunk and git_blame__entry

diff: include commit message when formatting patch

index: always queue `remove_entry` for removal

reset: perform the checkout before moving HEAD or the index

This keeps the state of the workdir the same as one from HEAD, removing
a source of possible confusion when calculating the work that is to be
done.

Use a typedef for the submodule_foreach callback.

tree: mark a tree as already sorted

This fits with the style for the rest of the project, but more
importantly, makes life easier for bindings authors who auto-generate
code.

When replacing an index with a new one, we need to iterate
through all index entries in order to determine which entries are
equal. When it is not possible to re-use old entries for the new
index, we move it into a list of entries that are to be removed
and thus free'd.

When we encounter a non-zero error code, though, we skip adding
the current index entry to the remove-queue. `INSERT_MAP_EX`,
which is the function last run before adding to the remove-queue,
may return a positive non-zero code that indicates what exactly
happened while inserting the element. In this case we skip adding
the entry to the remove-queue but still continue the current
operation, leading to a leak of the current entry.

Fix this by checking for a negative return value instead of a
non-zero one when we want to add the current index entry to the
remove-queue.

The trees are sorted on-disk, so we don't have to go over them
again. This cuts almost a fifth of time spent parsing trees.

CMakeLists: Compare CMAKE_SIZEOF_VOID_P as a number, not as a string

checkout test: Apply umask to file-mode test as well

tree: use a specialised mode parse function

index: canonicalize inserted paths safely