Might be related to JENKINS-13165 which is about ant excluding .git directories by default.

Looking at core/src/main/java/hudson/tasks/Fingerprinter.java record() calls

FileSet src = "">

The fix for the dirScanner was:

https://github.com/jenkinsci/jenkins/commit/0725d2765da789e02914deb4893a449eeda6a820

Which added an option to disable the default excludes, aka:

FileSet fs = Util.createFileSet(dir,includes,excludes);
fs.setDefaultexcludes(useDefaultExcludes);

The core/src/main/java/hudson/Util.java createFileSet() method does have an exclude which default to null but does not allow one to disable the useDefaultExcludes.

So I guess this bug is about porting the dirScanner fix to Util.createFileSet().

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