repo: remove an inappropriate use of PASSTHROUGH

repo: specify init.defaultbranch is meant to be a branch name

tests: fix variable name in list.c

Fix diff_entrycount -> diff_num_deltas doc typo

This just fixes a typo in the documentation, actual rename change was
done in 5f69a31f

We don't want the default branch's refname here but its name as branch.
Returning an error saying it's not a valid reference here suggests we want the
value of `init.defaultbranch` to be something like `refs/heads/default` which is
not the case.

This error code is for callbacks where we should act as though the callback was
not set. This is not something that makes sense for a `_foreach` and checking
for that error message to bubble up mostly is happenstance precisely because
this is not an error code we expect in the callback.

As part of removing this, let's also remove a use of foreach as we can open-code
this check.

Default to GIT_BRANCH_DEFAULT if init.defaultBranch is empty string

We already do this in repo_init_head

Remove duplicate line, in example code

tree: deprecate `git_treebuilder_write_with_buffer`

winhttp: skip certificate check if unable to send request

[skip ci]

commit-graph: Introduce `git_commit_graph_needs_refresh()`

commit-graph: Support lookups of entries in a commit-graph

The function `git_treebuilder_write_with_buffer` is unnecessary; it
is used internally as part of treebuilder writing, but it has little
use to external callers.  For callers that repeatedly write a
treebuilder, we can supply them with a buffer in the treebuilder struct
instead of recreating it.  For ourselves, when we want a single buffer
in our write loop, we can use an internal function.

merge: Check insert_head_ids error in create_virtual_base

Check git_signature_dup failure

insert_head_ids can fail due to allocation error

git_signature_dup can have an allocation failure

In some circumstances (e.g. when proxies are involved), winhttp will fail to reach the WINHTTP_CALLBACK_STATUS_SENDING_REQUEST phase. If this occurs, we'll error with ERROR_WINHTTP_INCORRECT_HANDLE_STATE when attempting to query the server certificate context (see https://docs.microsoft.com/en-us/windows/win32/api/winhttp/nf-winhttp-winhttpsendrequest#remarks).

To avoid this, verify that WinHttpSendRequest has reached the WINHTTP_CALLBACK_STATUS_SENDING_REQUEST phase before checking the certificate. Since we're using WinHTTP in synchronous mode, we know for sure that once WinHttpSendRequest returns we've either sent it successfully or not.

NOTE: WINHTTP_CALLBACK_STATUS_SENDING_REQUEST appears to be deprecated with no direct replacement. WINHTTP_CALLBACK_STATUS_SENDREQUEST_COMPLETE is only available in async mode, and there doesn't appear to be a method of querying this flag outside of the status callback.

Fix some typos

include: fix typos in comments

Fix documentation formating on repository.h

The enum 'git_repository_init_flag_t', 'git_repository_init_mode_t' and
the structure 'git_repository_init_options' does not follow the format
used by docurium.

index: Check git_vector_dup error in write_entries

This is for extra safety within write_entries

If allocating case_sorted.contents fails, git_vector_sort will segfault.

To prevent a race condition, these wlock/rlock calls should probably be checked
for errors.

Invert the workflow conditionals so that a workflow_dispatch event acts
like an on: push build.

Add new bindings for the R language