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The directory tree and the file table display the status of your working tree (and Index). The primary directory states are listed in Primary Directory States, and possible states of submodules in Submodule States. Every primary and submodule state may be combined with additional states, which are listed in Additional Directory States. The possible file states are listed in File States.

File Filtering

The Files table of the project window can be filtered by file state and name. The state filters can be set using the small toolbar buttons above the table as well as the menu items in the View menu. By default, if committable files (e.g. index-only changed or untracked) are hidden, the background turns to light-red as a reminder to not forget about them. If this annoys you because you permanently have untracked files in your working, you should consider to mark them as ignored. If this is no option for you, you can deactivate this coloring feature in the Preferences (page User Interface, option Use background color for the file table to indicate certain states).

To filter by name, use the input field (or <Ctrl/Cmd>+<F>-keystroke) above the file table. The context menu allows to enable regular expressions and save patterns for later usage or delete them. Even if unchanged files are hidden, they can be found by filtering by name - the files matching by name but not by state are shown in gray, while a light-yellow background indicates the name-filtering state.

Primary Directory States
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directory.states
directory.states

Image AddedDefaultDirectory is present in the repository (more precisely: there is at least one versioned file below this directory stored in the repository).
Image AddedUnversionedDirectory (and contained files) are present in the working tree, but have not been added to the repository yet. Use Stage to add the files to the repository.
Image AddedIgnoredDirectory is not present in the repository (exists only in the working tree) and is marked as to be ignored.
Image AddedMissingDirectory is present in the repository, but does not exist in the working tree. Use Stage to remove the files from the repository or Discard to restore them in the working tree.
Image AddedConflictRepository contains conflicting files (only displayed on the root directory). Use Resolve to resolve the conflict.
Image AddedMergeRepository is in 'merging' or 'rebasing' state (only displayed on the root directory). Either Commit the merge/rebase or use Discard to cancel the merge/rebase.
Image AddedRoot/SubmoduleDirectory is either the project root or a submodule root, see Submodule States.

Submodule States
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submodule.states
submodule.states

Image AddedSubmoduleUnchanged submodule.
Image AddedModified in working treeSubmodule in working tree points to a different commit than the one registered in the repository. Use Stage to register the new commit in the Index, or Reset to reset the submodule to the commit registered in the repository.
Image AddedModified in IndexSubmodule in working tree points to a different commit than the one registered in the repository, and this changed commit has been staged to the Index. Commit this change or use Discard to revert the Index.
Image AddedModified in WT and IndexSubmodule in working tree points to a different commit than the one in the Index, and the staged commit in the Index is different from the one in the repository. Use either Stage to register the changed commit in the Index (overwriting the Index change), Discard to revert the Index, or Reset to reset the submodule to the commit registered in the Index.
Image AddedForeign repositoryNested repository is not registered in the parent repository as submodule. Use Stage to register (and add) the submodule to the parent repository.

Additional Directory States
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directory.badges
directory.badges

Image AddedDirect Local ChangesThere are local (or Index) changes within the directory itself.
Image AddedIndirect Local ChangesThere are local (or Index) changes in one of the subdirectories of this directory.

File States
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file.states
file.states

Image AddedUnchangedFile is under version control and neither modified in working tree nor in Index.
Image AddedUnversionedFile is not under version control, but only exists in the working tree. Use Stage to add the file or Ignore to ignore the file.
Image AddedIgnoredFile is not under version control (exists only in the working tree) and is marked to be ignored.
Image AddedModifiedFile is modified in the working tree. Use Stage to add the changes to the Index or Commit the changes immediately.
Image AddedModified (Index)File is modified and the changes have been staged to the Index. Either Commit the changes or Unstage changes to the working tree.
Image AddedModified (WT and Index)File is modified in the working tree and in the Index in different ways. You may Commit either Index changes or working tree changes.
Image AddedModified (File Mode)The content of the file is not modified, but the executable bits are set different than in the repository. Refer to Fixing 'Modified (File Mode)' on Windows on how to fix that state on Windows.
Image AddedAddedFile has been added to Index. Use Unstage to remove from the Index.
Image AddedRemovedFile has been removed from the Index. Use Unstage to un-schedule the removal from the Index.
Image AddedMissingFile is under version control, but does not exist in the working tree. Use Stage or Remove to remove from the Index or Discard to restore in the wirking tree.
Image AddedModified (Added)File has been added to the Index and there is an additional change in the working tree. Use Commit to either commit just the addition or commit addition and change.
Image AddedIntent-to-AddFile is planned to be added to the Index. Use Add or Stage to add actually or Discard to revert to unversioned.
Image AddedConflictA merge-like command resulted in conflicting changes. Use the Conflict Solver to fix the conflicts.

Fixing 'Modified (File Mode)' on Windows
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file.states.how-to-fix-modified-file-mode
file.states.how-to-fix-modified-file-mode

On Windows, the Modified (File Mode) state is usually caused due to a misconfiguration of your local repository, when not having core.filemode configuration option explicitly set to false (the default value is true).

Hence, if this option in not present in .git/config of your repository, invoke git config core.filemode false in the root directory of your repository to fix this problem.