Add a configurable limit to the max pack size that will be indexed

Add a checkout example

In attempt to provide adequate Git command analogy in regards to
ignored files handling, `git_ignore_path_is_ignored` description
mentions doing `git add .` on directory containing the file, and
whether the file in question would be added or not - but behavior of
the two matches for untracked files only, making the comparison
misleading in general sense.

For tracked files, Git doesn't subject them to ignore rules, so even
if a rule applies, `git add .` would actually add the tracked file
changes to index, while `git_ignore_path_is_ignored` would still
consider the file being ignored (as it doesn't check the index, as
documented).

Let's provide `git check-ignore --no-index` as analogous Git command
example instead, being more aligned with what `git_ignore_path_is_ignored`
is about, no matter if the file in question is already tracked or not.

See issue #4720 (git_ignore_path_is_ignored documentation
misleading?, 2018-07-10)[1] for additional information.

[1] https://github.com/libgit2/libgit2/issues/4720

As git_annotated_commit seems to behave like cgit's refish, it's quite
helpful to abstract away "targets" via git_annotated_commit_from_id/from_ref.
As the former is accessible via git_annotated_commit_id, make the latter
also available to users.

Add a "dirty" state to the index when it has unsaved changes

Add the `GIT_OPT_ENABLE_UNSAVED_INDEX_SAFETY` option, which will cause
commands that reload the on-disk index to fail if the current
`git_index` has changed that have not been saved.  This will prevent
users from - for example - adding a file to the index then calling a
function like `git_checkout` and having that file be silently removed
from the index since it was re-read from disk.

Now calls that would re-read the index will fail if the index is
"dirty", meaning changes have been made to it but have not been written.
Users can either `git_index_read` to discard those changes explicitly,
or `git_index_write` to write them.

When the index is dirty, return GIT_EINDEXDIRTY so that consumers can
identify the exact problem programatically.

Fix typo

Fix some type issues

More fixes

Address requested changes

Add test

Fix naming

Fix condition and tests

Address requested changes

Fix typo