Not able to add new github projects with sparse checkout of folder

[jkjha]

Update
Below issue seems to be happening only with the projects with sparse checkout of git repo. For other projects, it seems to work fine.

I am running a opengrok docker instance with many projects... however after recent opengrok version upgrade and few unrelated changes (OS upgrade where code reside), the indexer command started failing. I see error only in history command, but it doesnt create either data/xref/ or index data.

I see below error in log:

Sep 20, 2025 12:50:11 PM org.opengrok.indexer.history.HistoryGuru lambda$createHistoryCacheReal$36
WARNING: failed to create history cache for {dir='/opengrok/src/project_name.github.devops',type=git,history=on,historyCache=on,merge=true,annotationCache=off,tagsEnabled=off}
org.eclipse.jgit.api.errors.JGitInternalException: Error while parsing attributes
	at org.eclipse.jgit.treewalk.TreeWalk.getAttributes(TreeWalk.java:635)
	at org.eclipse.jgit.treewalk.TreeWalk.getAttributes(TreeWalk.java:589)
	at org.eclipse.jgit.diff.DiffEntry.scan(DiffEntry.java:169)
	at org.eclipse.jgit.diff.DiffEntry.scan(DiffEntry.java:110)
	at org.eclipse.jgit.diff.DiffEntry.scan(DiffEntry.java:87)
	at org.eclipse.jgit.diff.DiffFormatter.scan(DiffFormatter.java:533)
	at org.opengrok.indexer.history.GitRepository.getFilesBetweenCommits(GitRepository.java:649)

To Reproduce
Place the folder in /opengrok/src/<project_name> and start the indexer command :

Example command that I run manually (it runs automatically bu container):

opengrok-reindex-project -J=-XX:-UseGCOverheadLimit -J=-Xmx36g -J=-server --printoutput --api_timeout 300 --jar /opengrok/lib/opengrok.jar -t /opengrok/etc/logging.properties.template -d /opengrok/log/project_name.github.devops -U http://localhost:8080/ -P project_name.github.devops -- --connectTimeout 300 -r dirbased -G -m 4096 --leadingWildCards on -c /usr/local/bin/ctags -o /opengrok/etc/ctags.config -U http://localhost:8080/ -H project_name.github.devops

Expected behavior
Indexing should work normally and it should create "/opengrok/data/xref/project_name.github.devops, /opengrok/data/index/project_name.github.devops etc.

Full log

Sep 20, 2025 12:49:40 PM org.opengrok.indexer.configuration.Configuration read
INFO: Reading configuration from '/tmp/tmpb7qpb63v'
Sep 20, 2025 12:49:41 PM org.opengrok.indexer.index.Indexer parseOptions
INFO: Indexer options: [-R, /tmp/tmpb7qpb63v, --connectTimeout, 300, -r, dirbased, -G, -m, 4096, --leadingWildCards, on, -c, /usr/local/bin/ctags, -o, /opengrok/etc/ctags.config, -U, http://localhost:8080/, -H, project_name.github.devops]
INFO: file with extra options for ctags: /opengrok/etc/ctags.config
SLF4J(W): No SLF4J providers were found.
SLF4J(W): Defaulting to no-operation (NOP) logger implementation
SLF4J(W): See https://www.slf4j.org/codes.html#noProviders for further details.
Sep 20, 2025 12:49:42 PM org.opengrok.indexer.util.Statistics logIt
INFO: Done invalidating repositories (1 valid, 1 working) (took 529 ms)
Sep 20, 2025 12:49:42 PM org.opengrok.indexer.index.Indexer runMain
INFO: Indexer version 1.14.2 (4c5dc2465cb0729dfe0fc765d8bd7cf99ee82e91) running on Java version: 21.0.8+9-LTS, name: OpenJDK 64-Bit Server VM, vendor: Eclipse Adoptium, arch: amd64 with properties: ncpu: 14, maxMemory: 36.0 GiB
Sep 20, 2025 12:49:42 PM org.opengrok.indexer.configuration.RuntimeEnvironment validateUniversalCtags
INFO: Using ctags: Universal Ctags 6.2.0(df6a390df), Copyright (C) 2015-2025 Universal Ctags Team
Universal Ctags is derived from Exuberant Ctags.
Exuberant Ctags 5.8, Copyright (C) 1996-2009 Darren Hiebert
  Compiled: Aug 29 2025, 08:33:35
  URL: https://ctags.io/
  Output version: 1.1
  Optional compiled features: +wildcards, +regex, +iconv, +option-directory, +xpath, +yaml, +packcc, +optscript
Sep 20, 2025 12:49:42 PM org.opengrok.indexer.index.Indexer prepareIndexer
INFO: Generating history cache for repositories: /project_name.github.devops
Sep 20, 2025 12:49:42 PM org.opengrok.indexer.history.HistoryGuru createHistoryCacheReal
INFO: Creating history cache for 1 repositories
Sep 20, 2025 12:49:42 PM org.opengrok.indexer.history.HistoryGuru createHistoryCache
INFO: Creating history cache for {dir='/opengrok/src/project_name.github.devops',type=git,history=on,historyCache=on,merge=true,annotationCache=off,tagsEnabled=off}
Sep 20, 2025 12:50:11 PM org.opengrok.indexer.history.HistoryGuru lambda$createHistoryCacheReal$36
WARNING: failed to create history cache for {dir='/opengrok/src/project_name.github.devops',type=git,history=on,historyCache=on,merge=true,annotationCache=off,tagsEnabled=off}
org.eclipse.jgit.api.errors.JGitInternalException: Error while parsing attributes
	at org.eclipse.jgit.treewalk.TreeWalk.getAttributes(TreeWalk.java:635)
	at org.eclipse.jgit.treewalk.TreeWalk.getAttributes(TreeWalk.java:589)
	at org.eclipse.jgit.diff.DiffEntry.scan(DiffEntry.java:169)
	at org.eclipse.jgit.diff.DiffEntry.scan(DiffEntry.java:110)
	at org.eclipse.jgit.diff.DiffEntry.scan(DiffEntry.java:87)
	at org.eclipse.jgit.diff.DiffFormatter.scan(DiffFormatter.java:533)
	at org.opengrok.indexer.history.GitRepository.getFilesBetweenCommits(GitRepository.java:649)
	at org.opengrok.indexer.history.GitRepository.getFilesForCommit(GitRepository.java:615)
	at org.opengrok.indexer.history.GitRepository.traverseHistory(GitRepository.java:544)
	at org.opengrok.indexer.history.RepositoryWithHistoryTraversal.doCreateCache(RepositoryWithHistoryTraversal.java:194)
	at org.opengrok.indexer.history.Repository.createCache(Repository.java:403)
	at org.opengrok.indexer.history.HistoryGuru.createHistoryCache(HistoryGuru.java:1078)
	at org.opengrok.indexer.history.HistoryGuru.lambda$createHistoryCacheReal$36(HistoryGuru.java:1122)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
	at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: org.eclipse.jgit.errors.MissingObjectException: Missing blob 6bd7389c8ac39c614e8ffdfd075f2ca8bbb83e6d
	at org.eclipse.jgit.internal.storage.file.WindowCursor.open(WindowCursor.java:138)
	at org.eclipse.jgit.treewalk.CanonicalTreeParser.loadAttributes(CanonicalTreeParser.java:393)
	at org.eclipse.jgit.treewalk.CanonicalTreeParser.findAttributes(CanonicalTreeParser.java:385)
	at org.eclipse.jgit.treewalk.CanonicalTreeParser.getEntryAttributesNode(CanonicalTreeParser.java:375)
	at org.eclipse.jgit.attributes.AttributesHandler.attributesNode(AttributesHandler.java:402)
	at org.eclipse.jgit.attributes.AttributesHandler.mergePerDirectoryEntryAttributes(AttributesHandler.java:232)
	at org.eclipse.jgit.attributes.AttributesHandler.getAttributes(AttributesHandler.java:144)
	at org.eclipse.jgit.treewalk.TreeWalk.getAttributes(TreeWalk.java:631)
	... 16 more

Sep 20, 2025 12:50:11 PM org.opengrok.indexer.util.Statistics logIt
INFO: Done history cache for all repositories (took 29.252 seconds)
Sep 20, 2025 12:50:11 PM org.opengrok.indexer.index.Indexer prepareIndexer
INFO: Done generating history cache
Sep 20, 2025 12:50:11 PM org.opengrok.indexer.util.Statistics logIt
INFO: Done invalidating repositories (1 valid, 1 working) (took 79 ms)
Sep 20, 2025 12:50:11 PM org.opengrok.indexer.index.Indexer doIndexerExecution
INFO: Starting indexing
Sep 20, 2025 12:50:11 PM org.apache.lucene.store.MemorySegmentIndexInputProvider <init>
INFO: Using MemorySegmentIndexInput with Java 21; to disable start with -Dorg.apache.lucene.store.MMapDirectory.enableMemorySegments=false
Sep 20, 2025 12:50:11 PM org.opengrok.indexer.index.IndexDatabase addIndexDatabaseForProject
SEVERE: Failed to create history cache for some repositories of project project_name.github.devops:indexed=false,history=true: {{dir='/opengrok/src/p2v.tera.vcf.main.github-...
Sep 20, 2025 12:50:11 PM org.opengrok.indexer.index.Indexer doIndexerExecution
INFO: Waiting for the executors to finish
Sep 20, 2025 12:50:11 PM org.opengrok.indexer.util.Statistics logIt
INFO: Done indexing data of all repositories (took 37 ms)
Sep 20, 2025 12:50:11 PM org.opengrok.indexer.util.Statistics logIt
INFO: Indexer finished (took 31.30 seconds)
Sep 20, 2025 12:50:11 PM org.opengrok.indexer.index.Indexer runMain
INFO: Indexer finished with success

Additional context
Opengrok image: 1.14.1
Indexer running on centos(rocky9)