The tracking issue if this causes problems is
https://gitlab.com/gitlab-org/gitaly/issues/1028

When the applied diff contains UTF-8 or some other encoded data, the diff
returned back from the git process may be in ASCII-8BIT format. Writing this
data to stdin may fail if the data because stdin expects this data to be in
UTF-8. By switching the output to binmode, we ensure that the diff will
always be written as-is.

Closes gitlab-org/gitlab-ee#4960

		    #	modified:   lib/gitlab/git/commit.rb

Closes gitaly#985

The refs hash is used to determine what branches and tags have a commit
as head in the network graph. The previous implementation depended on
Rugged#references. The problem with this implementation was that it
depended on rugged, but also that it iterated over all references and
thus loading more data than needed if for example the project uses CI/CD
environments, Pipelines, or Merge Requests.

Given only refs are checked the network cares about the GraphHelper#refs
method has no need to reject those, simplifying the method.

Closes gitlab-org/gitaly#880

Signed-off-by: NBastian Blank <waldi@debian.org>

Uses Lfs::FileModificationHandler to coordinate LFS detection, creation of LfsObject, etc

Caveats:
 1. This isn't used by the multi-file editor / Web IDE
 2. This isn't used on rename. We'd need to be able to download LFS files
    and add them to the commit if they no longer match so not as simple.
 3. We only check the root .gitattributes file, so this should be improved
    to correctly check for nested .gitattributes files in subfolders.

We stop relying on Gitlab::Git::Env for the RevList class, and use
Gitlab::Git::Repository#run_git methods inteaad. The refactor also fixes
another issue, since we now top using "path_to_repo" (which is a
Repository model method).

This was affecting the performance of `Gitlab::Git::Repository#squash`.

As part of gitlab-org/gitaly#884, this commit contains the client
implementation for both TagNamesContaintingCommit and
BranchNamesContainingCommit. The interface in the Repository model stays
the same, but the implementation on the serverside, e.g. Gitaly, uses
`for-each-ref`, as opposed to `branch` or `tag` which both aren't
plumbing command. The result stays the same.

On the serverside, we have the opportunity to limit the number of names
to return. However, this is not supported on the front end yet. My
proposal to use this ability: gitlab-org/gitlab-ce#42581. For now, this
ability is not used as that would change more behaviours on a feature
flag which might lead to unexpected changes on page refresh for example.

- Add tests for Repository#write_config

Closes gitaly#967

Fixes #42544

Closes gitaly#958

This reverts merge request !16525

Related to #39805

Closes gitaly#921

Closes gitaly#946

Closes gitaly#929