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Fix out-of-tree tests

Tony Finch requested to merge 3536-out-of-tree into main

The change to in commit 258a896a broke the system tests in out-of-tree builds because is not copied to the worktree. Use instead.

Also, I noticed that the configure script's check for the CHANGES timestamp was incorrect for out-of-tree builds, so I have fixed that as well.

Closes #3536 (closed)

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