Possible flake fix

[jglick]

This flake from #1504 seems to be a test problem

Z:\agent\workspace\hub-branch-source-plugin_PR-1504\target\tmp\j h6248222677314807097\jobs\test0\indexing\indexing.log: The process cannot access the file because it is being used by another process

  64.126 [id=28]	WARNING	o.j.h.t.RemainingActivityListener#onTearDown: BranchIndexing[test0] still seems to be running, which could break deletion of log files or metadata

The patch addresses the warning at least, so may fix the flake as well.

[jglick]

https://github.com/jenkinsci/github-branch-source-plugin/pull/1508/checks?check_run_id=69441217258 apparently that did not work

[jtnord]

if it helps at all, if the log uses RewindableFileOutputStream or its rotating variant, there are issues as the logs are not really closed on close and can be magically reopened after closure by an arbitrary write. Same happened with agent logs.
So the indexing thread needs to be stopped before the log is closed.