(Re)Indexation not working

[Sironas]

Hello,

I have currently a problem with OpenGrok 1.13.4.

The first indexation of the code went perfectly and everything was fine. But after several days we noticed that code was missing from indexing. I search a little and it seems that the reindexation (automatic or not) doesn't seem to index new files or probably all kinds of difference after the first indexation (it's obvious on new classes not showing in the search).

When I execute opengrok-indexer or opengrok-reindex-project it goes through indexing my project but does nothing

opengrok-indexer --jar /opengrok/lib/opengrok.jar -- -c /usr/local/bin/ctags -s /opengrok/src -d /opengrok/data -H -P -S -G --renamedHistory on -R /opengrok/etc/configuration.xml -U http://localhost:8080 --depth 10

INFO: Starting file collection using history traversal for directory '/meteodyn_development'
Jun 11, 2024 12:05:57 PM org.opengrok.indexer.util.Statistics logIt
INFO: Done file collection for directory '/meteodyn_development' (took 0 ms)
INFO: Starting indexing of directory '/meteodyn_development'
Jun 11, 2024 12:05:59 PM org.opengrok.indexer.util.Statistics logIt
INFO: Done indexing of directory '/meteodyn_development' (took 0 ms)

While searching I found a parameter to check indexes so I run it and here it says there is some problem on my project. When using --checkIndex documents I got the following errors

WARNING: index check failed
index '/opengrok/data/index/meteodyn_development' failed document check: missing paths = [/opengrok/src/meteodyn_development/common/vp_business/business_datahub/MTDDatahubServices/Services/Anemos/MTDDataHubAnemosSettings.cs, /opengrok/src/meteodyn_de...
        at org.opengrok.indexer.index.IndexCheck.checkDocuments(IndexCheck.java:604)
        at org.opengrok.indexer.index.IndexCheck.checkDir(IndexCheck.java:277)
        at org.opengrok.indexer.index.IndexCheck.checkDirWithLogging(IndexCheck.java:247)
        at org.opengrok.indexer.index.IndexCheck.lambda$checkProjectsParallel$0(IndexCheck.java:153)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:840)

Index check failed
You might want to remove [/opengrok/src/meteodyn_development]
Indexer command failed (return code 1)

If I check the first class, it was indeed moved somewhere else so this path doesn't exist anymore

I activated the automatic synchronization with SYNC_PERIOD_MINUTES=20 on the docker compose (env variable). I notice that every 20 minutes all my projects are updating (symbole ! in the web view), I also notice that all my repositories are correctly updated so the mirror part of the script works fine.

I don't know what's going wrong here and what I should do as launching the reindex doesn't work, and I don't want to reindex everything everyday that's not the point. I thought that the periodic synchronization could update just the delta of modification, isn't that supposed to be the case ?

I probably do something wrong here, but I can't figure what...

My tree under /opengrok/src/meteodyn_development maybe is the cause of everything as this is not the root of my repository but a folder containing others folders and in them several repositories. I did that for the web view to show only one project from all those repositories

example:

/opengrok/src/meteodyn_development/common/dir1/repo1
/opengrok/src/meteodyn_development/common/dir1/repo2
/opengrok/src/meteodyn_development/common/dir2/repo3
...

Thank you for you help

Thomas