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Build 16039 (SmartGit 20.2 preview) will remove these ANSI sequences to make the text easier to read.

Could you please provide us with a test repository where we can reproduce the problem?

What exactly should happen if such an entry is clicked - if SmartGit is running and not running?

Sorry, I misunderstood you. I thought you don't want to see them in the Graph, but you want to hide them in the Branches view. Fortunately, there exists a solution for that. Please add following lines to the .git/config:

[smartgit "refLimit"]

    remoteBranchIncludeRegEx =

    remoteBranchExcludeRegEx =
    tagIncludeRegEx =
    tagExcludeRegEx = build-\\d{4}

and configure the values at the right.

In SmartGit you can show/hide any ref you like - see the checkboxes in front of the refs in the Branches view.

If the worktree directory has already been deleted, use Repository | Prune Obsolete Worktrees from one of the other worktrees or the main repository.

SmartGit just reopens all the repositories (in one window) that were open before exiting, even if they were open in different windows. I reckon, you can't open multiple windows in SourceTree.