I'll look at those closer - thanks for the links. Here are the logs from the server:
2016-07-13 02:37:32 [INFO ] 18 repository models loaded for darmbrust in 14 msecs
org.eclipse.jgit.errors.MissingObjectException: Missing blob 0000000000000000000000000000000000000000
at org.eclipse.jgit.internal.storage.file.WindowCursor.getObjectSize(WindowCursor.java:167)
at com.gitblit.models.PathModel$PathChangeModel.from(PathModel.java:181)
at com.gitblit.utils.JGitUtils.getFilesInCommit(JGitUtils.java:1048)
at com.gitblit.utils.JGitUtils.getFilesInCommit(JGitUtils.java:985)
at com.gitblit.service.LuceneService.index(LuceneService.java:648)
at com.gitblit.service.LuceneService.updateIndex(LuceneService.java:847)
at com.gitblit.service.LuceneService.index(LuceneService.java:220)
at com.gitblit.service.LuceneService.run(LuceneService.java:186)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
org.eclipse.jgit.errors.MissingObjectException: Missing blob 0000000000000000000000000000000000000000
at org.eclipse.jgit.internal.storage.file.WindowCursor.getObjectSize(WindowCursor.java:167)
at com.gitblit.models.PathModel$PathChangeModel.from(PathModel.java:181)
at com.gitblit.utils.DiffUtils$DiffStat.addPath(DiffUtils.java:169)
at com.gitblit.utils.DiffStatFormatter.format(DiffStatFormatter.java:48)
at com.gitblit.utils.JGitUtils.getFilesInCommit(JGitUtils.java:1052)
at com.gitblit.utils.JGitUtils.getFilesInCommit(JGitUtils.java:985)
at com.gitblit.service.LuceneService.index(LuceneService.java:648)
at com.gitblit.service.LuceneService.updateIndex(LuceneService.java:847)
at com.gitblit.service.LuceneService.index(LuceneService.java:220)
at com.gitblit.service.LuceneService.run(LuceneService.java:186)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)