We have multiple projects, and each project can have repositories, with each repository having difference source files... etc...
We need a way to make a clone of all these items without having to go to each single folder/file. Is there an easier way to do this?
Welcome to the Atlassian Community.
Short answer is no, it is not possible. You can get halfway there by using custom actions that run a script that clones all your repositories, but you cannot create the bookmarks in Sourcetree for them, that is a manual process.