Safely deprecate `git_transfer_progress` and `git_transfer_progress_cb`
types, forwarding them to the new `git_indexer_progress` and
`git_indexer_progress_cb`.

Update internal usage of `git_transfer_progress` to
`git_indexer_progreses`.

The name `git_transfer_progress` does not reflect its true purpose.

It suggests that it's progress for a non-existence `git_transfer`
object, and is used for indexing callbacks more broadly than just
during transfers.

Rename `git_transfer_progress` to `git_indexer_progress`.

Right now, we simply turn on connectivity checks in the indexer as soon
as we have access to an object database. But seeing that the
connectivity checks may incur additional overhead, we do want the user
to decide for himself whether he wants to allow those checks.
Furthermore, it might also be desirable to check connectivity in case
where no object database is given at all, e.g. in case where a fully
connected pack file is expected.

Add a flag `verify` to `git_indexer_options` to enable additional
verification checks. Also avoid to query the ODB in case none is given
to allow users to enable checks when they do not have an ODB.

We strive to keep an options structure to many functions to be able to
extend options in the future without breaking the API. `git_indexer_new`
doesn't have one right now, but we want to be able to add an option
for enabling strict packfile verification.

Add a new `git_indexer_options` structure and adjust callers to use
that.

It was there to keep it apart from the one which read in from a file on
disk. This other indexer does not exist anymore, so there is no need for
anything other than git_indexer to refer to it.

While here, rename _add() function to _append() and _finalize() to
_commit(). The former change is cosmetic, while the latter avoids
talking about "finalizing", which OO languages use to mean something
completely different.

When given an ODB from which to read objects, the indexer will attempt
to inject the missing bases at the end of the pack and update the
header and trailer to reflect the new contents.

Fixed a few header @param and @return typos with the help of -Wdocumentation in Xcode.

The following warnings have not been fixed:
common.h:213 - Not sure how the documentation format is for '...'
notes.h:102 - Correct @param name but empty text
notes.h:111 - Correct @param name but empty text
pack.h:140 - @return missing text
pack.h:148 - @return missing text