Cant speak for industry, but We have a Mixed mode SoC flow that includes digital flows. Everything stored in Git version control:
Steps:
1. Import analog macros from repository to Virtuoso environment. (no open sorce tools yet)
2. Run all digital flows if needed, and import the results to Virtuoso.
3. LVS
4. Tiling
5. LVS
6. DRC
7. Notification
Everything is configured with a 'configure' scripts.
Steps are executed with 'make'
It is like software compilation, but for hardware. Tools exist: 'bash' and 'make'. The rest is matter of EDA software API's.