[java] Why does Eclipse Java Package Explorer show question mark on some classes?

those icons are a way of Egit to show you status of the current file/folder in git. You might want to check this out:

image describing Eclipse icons for Egit

  • dirty (folder) - At least one file below the folder is dirty; that means that it has changes in the working tree that are neither in the index nor in the repository.
  • tracked - The resource is known to the Git repository. untracked - The resource is not known to the Git repository.
  • ignored - The resource is ignored by the Git team provider. Here only the preference settings under Team -> Ignored Resources and the "derived" flag are relevant. The .gitignore file is not taken into account.
  • dirty - The resource has changes in the working tree that are neither in the index nor in the repository.
  • staged - The resource has changes which are added to the index. Not that adding to the index is possible at the moment only on the commit dialog on the context menu of a resource.
  • partially-staged - The resource has changes which are added to the index and additionally changes in the working tree that are neither in the index nor in the repository.
  • added - The resource is not yet tracked by but added to the Git repository.
  • removed - The resource is staged for removal from the Git repository.
  • conflict - A merge conflict exists for the file.
  • assume-valid - The resource has the "assume unchanged" flag. This means that Git stops checking the working tree files for possible modifications, so you need to manually unset the bit to tell Git when you change the working tree file. This setting can be switched on with the menu action Team->Assume unchanged (or on the command line with git update-index--assume-unchanged).

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