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With respect to issue #1, new SVNKit 1.7 was dropping the root cause of the exception, which makes it difficult for us to get to the root cause. I fixed this in SVNKit 1.7.4-jenkins-3, which will be a part of Subversion plugin 1.41 that I'll be releasing shortly. So I request those who are seeing this issue to upgrade to 1.41 and report the stack trace, including all the "Caused by ..." sections.
With respect to issue #2, I couldn't reproduce it. This issue is independent from issue #1, so I request that the submitter (or anyone else seeing the issue) to open a separate ticket, with details, such as the type of the repository you check out from, Subversion server version, and the console output.
With respect to Issue #3, this was presumably because the user set the workspace format to 1.7, and that was stored in the configuration file, but Subversion 1.39 (that doesn't support 1.7 workspace) didn't recognize this value and failed to gracefully recover from it. We cannot retroactively fix 1.39, but in case similar issue happens in the future, I put a fix in 1.41 to fall back to 1.4.
These 3 issues are independent issues, and so we'll use this ticket to track the issue #1 portion of the original bug report.
If people see what's discussed in the issue #2 and #3, please open separate tickets to avoid confusion (but please do post those new ticket IDs so that other people who want to comment on those sub-issues know where to go.)