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Since 3.4.5 and in 3.4.6 Sourcetree has been unable to clone a bare repository from Bitbucket Server. Downgrading to 3.4.4 solves the problem. This happens with both embedded and external Git. When I paste an address, a circle starts spinning next to Advanced Options, then it freezes momentarily and crashes. It works normally when cloning a repository with data.
Workaround for me is to clone the repository via command line and then add it to Sourcetree. Sourcetree itself works with bare repositories normally.