gitaly: Migrate away from `[gitlab-shell]` configuration section

What does this MR do?

Gitaly has deprecated the [gitlab-shell] section. This section contained a single key dir from which two different paths were derived:

- The path of the file that contains the token required to connect
  to the GitLab API. This path is obtained by joining the directory
  path with ".gitlab_shell_secret". The setting has been replaced by
  a `[gitlab] secret_file` key.

- The path of the directory that contains custom Git hooks. This
  path is obtained by joining the directory with "hooks". This
  setting has been replaced by a `[hooks] custom_hooks_dir` key.

Adjust the generated configuration file to make use of those new keys so that Gitaly can eventually remove the old section. This refactoring is not expected to cause any change in behaviour as we configure the new settings to point to the exact same locations that the old setting did.

Part of Migrate away from `[gitlab-shell]` configuration (gitaly#4250).

Related issues

Checklist

See Definition of done.

For anything in this list which will not be completed, please provide a reason in the MR discussion.

Required

• MR title and description are up to date, accurate, and descriptive.
• MR targeting the appropriate branch.
• Latest Merge Result pipeline is green.
• When ready for review, MR is labeled "~workflow::ready for review" per the Distribution MR workflow.

For GitLab team members

If you don't have access to this, the reviewer should trigger these jobs for you during the review process.

• The manual Trigger:ee-package jobs have a green pipeline running against latest commit.
• If config/software or config/patches directories are changed, make sure the build-package-on-all-os job within the Trigger:ee-package downstream pipeline succeeded.
• If you are changing anything SSL related, then the Trigger:package:fips manual job within the Trigger:ee-package downstream pipeline must succeed.
• If CI configuration is changed, the branch must be pushed to dev.gitlab.org to confirm regular branch builds aren't broken.

Expected (please provide an explanation if not completing)

• Test plan indicating conditions for success has been posted and passes.
• Documentation created/updated.
• Tests added.
• Integration tests added to GitLab QA.
• Equivalent MR/issue for the GitLab Chart opened.
• Validate potential values for new configuration settings. Formats such as integer 10, duration 10s, URI scheme://user:passwd@host:port may require quotation or other special handling when rendered in a template and written to a configuration file.