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2.2. Import Team Project Set (*.psf) should use the default repository folder specified on the 'Git' preference page. For this, the preference org.eclipse.egit.ui.UIPreferences.DEFAULT_REPO_DIR has to be moved to the core bundle together with migration code that transfers the current value from UI to Core. See also bug 384998.
Same bug via File > Import... > Plug-ins and Fragments, and then select "Projects from a repository": The cloned repo ends up directly inside the workspace rather than at the configured location.
Still in 4.1. I will try to take a look at it.
New Gerrit change created: https://git.eclipse.org/r/52570
Gerrit change https://git.eclipse.org/r/52570 was merged to [master]. Commit: http://git.eclipse.org/c/egit/egit.git/commit/?id=1332a1fedf6a2f189eb90644946a7309423eccf3
submitted patch
*** Bug 478564 has been marked as a duplicate of this bug. ***