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code from HEAD If you set a breakpoint in "remote" source (source that does not exist in the workspace) and restart the workspace the breakpoints are removed. This is expected (albeit wrong) because the source really does not exist anymore - but we must find a way to persist breakpoint(s) even for those whose backing resource no longer exists.
Our new external source handling has resolved this issue. You can set bps in the local or non-local source and they are persisted as expected.