In the 1.+ version of SourceTree, we were able to remove a project from bookmark, and then find it again in our bookmarks when we re-open it.
On the current version of SourceTree, if I delete a repo from the "All Repos", and then if I open it again, the repo does not reappear in the "All Repos".
The only workaround that I found was to clone again the project in order to make it appear in my "All repos" folder.
My question is: how can I save a repository to my bookmarks without recloning it ?
I'm afraid I don't quite follow the question, could you add some more detail maybe screenshots to clarify?
In both versions of SourceTree you can delete a bookmark and you have the option to just remove the bookmark and/or delete the repository from the filesystem as well.
If you remove a bookmark, but not the repository you can use the 'Add' option to recreate the bookmark.
Alternatively if you move a repository on the file system but leave the bookmark, yu can double-click on the bookmark and point it at the new repository location
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