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Can we make any control to atlantis workflow let's say first i want to run vpc plan then it works only create subnets plan

You can do this with a custom workflow either in the server-side config or in the atlantis.yaml in the repository itself.

You want to set execution group

How can i set this @RB

See the docs https://www.runatlantis.io/docs/repo-level-atlantis-yaml.html#order-of-planning-applying

This is very hard to manage if i have a large number of folders. I am using terragrunt-atlantis-config generator so it automatically creates server side config so it is creating each folder as each project.

Yes that does seem difficult. Please feel free to propose a solution and/or create a ticket