Follow-up Comment #1, sr #1880 (project savane):
It much depends on the tool you use.
As far as Savane is concerned, you can export trackers items to an XML
format, and frontend data is otherwise stored in a classical MySQL database.
Your source code itself will be managed with a VCS such as Git or SVN, which
is independent of Savane. Nowadays it is increasingly easier to switch
between VCSes thanks to their import/export features, or failing that, by
using the "Tailor" converter.
Which CDE are you contemplating using?
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