Update Omnibus, CNG with new gitlab shell config values

In !1293 (merged), we moved gitlab shell log config values to the gitaly config.toml. We need to modify omnibus and cng to have default values in those config files.

• GDK (gitlab-development-kit!856 (merged))
• source installations (gitlab!18822 (merged))
• ensure new logs will go to ELK (https://gitlab.com/gitlab-com/gl-infra/infrastructure/issues/8192)
• omnibus (omnibus-gitlab!3680 (merged))
• CNG (gitlab-org/build/CNG!297 (merged))
• helm charts (gitlab-org/charts/gitlab!1004 (merged))

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Do not ship omnibus config change before checking with gitlab.com infra team that the new logs will automatically go into ELK!