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Untracked files will be lost if they are in a newly created directory

See original GitHub issue

Description

When I committed portion of the code, some of the untracked files suddenly disappeared. I found that if an entire folder is untracked, the folder will disappear after running lint-staged.

Steps to reproduce

├─staged-a
└─unstaged-folder-b
   └─unstaged-file-c

run lint-staged will lose unstaged-folder-b unstaged-file-c

Debug Logs

expand to view

C:/Users/Kunduin/Documents/GitHub/vue-space/src/components/VsInput/index.tsx will be removed VsInput is a newly untracked folder, index.tsx is a newly untracked file

> lint-staged -d

  lint-staged:bin Running `lint-staged@10.0.0-1` +0ms
  lint-staged Loading config using `cosmiconfig` +0ms
  lint-staged Successfully loaded config from `C:\Users\Kunduin\Documents\GitHub\vue-space\package.json`:
  lint-staged {
  lint-staged   '{stories,src}/**/*.scss': 'stylelint --syntax=scss',
  lint-staged   '{stories,src}/**/*.{ts,tsx,js}': 'prettier --write'
  lint-staged } +6ms
  lint-staged:cfg Validating config +0ms
Running lint-staged with the following config:
{
  '{stories,src}/**/*.scss': 'stylelint --syntax=scss',
  '{stories,src}/**/*.{ts,tsx,js}': 'prettier --write'
}
  lint-staged:run Running all linter scripts +0ms
  lint-staged:git Running git command [ 'rev-parse', '--show-toplevel' ] +0ms
  lint-staged:run Resolved git directory to be `C:/Users/Kunduin/Documents/GitHub/vue-space` +100ms
  lint-staged:git Running git command [ 'diff', '--staged', '--diff-filter=ACMR', '--name-only' ] +89ms
  lint-staged:run Loaded list of staged files in git:
  lint-staged:run [ 'src/components/VsButton/index.tsx' ] +83ms
  lint-staged:gen-tasks Generating linter tasks +0ms
  lint-staged:gen-tasks Generated task:
  lint-staged:gen-tasks {
  lint-staged:gen-tasks   pattern: '{stories,src}/**/*.scss',
  lint-staged:gen-tasks   commands: 'stylelint --syntax=scss',
  lint-staged:gen-tasks   fileList: []
  lint-staged:gen-tasks } +4ms
  lint-staged:gen-tasks Generated task:
  lint-staged:gen-tasks {
  lint-staged:gen-tasks   pattern: '{stories,src}/**/*.{ts,tsx,js}',
  lint-staged:gen-tasks   commands: 'prettier --write',
  lint-staged:gen-tasks   fileList: [
  lint-staged:gen-tasks     'C:/Users/Kunduin/Documents/GitHub/vue-space/src/components/VsButton/index.tsx'
  lint-staged:gen-tasks   ]
  lint-staged:gen-tasks } +2ms
Preparing... [started]
  lint-staged:git Backing up original state... +0ms
  lint-staged:file Trying to access `C:\Users\Kunduin\Documents\GitHub\vue-space\.git\MERGE_HEAD` +0ms
  lint-staged:file Unable to access file `C:\Users\Kunduin\Documents\GitHub\vue-space\.git\MERGE_HEAD` with error: +6ms
  lint-staged:file Error: ENOENT: no such file or directory, access 'C:\Users\Kunduin\Documents\GitHub\vue-space\.git\MERGE_HEAD' +15ms
  lint-staged:git Running git command [ 'ls-files', '--others', '--exclude-standard' ] +120ms
  lint-staged:git Detected untracked files: +104ms
  lint-staged:git .storybook/tsconfig.json
  lint-staged:git src/components/VsInput/index.tsx +1ms
  lint-staged:git Backing up untracked files... +1ms
  lint-staged:file Reading buffer from file `C:/Users/Kunduin/Documents/GitHub/vue-space/.storybook/tsconfig.json` +85ms
  lint-staged:file Reading buffer from file `C:/Users/Kunduin/Documents/GitHub/vue-space/src/components/VsInput/index.tsx` +0ms
  lint-staged:file Done reading buffer from file `C:/Users/Kunduin/Documents/GitHub/vue-space/.storybook/tsconfig.json`! +1ms
  lint-staged:file Done reading buffer from file `C:/Users/Kunduin/Documents/GitHub/vue-space/src/components/VsInput/index.tsx`! +1ms
  lint-staged:git Done backing up untracked files! +4ms
  lint-staged:git Running git command [
  'stash',
  'save',
  '--quiet',
  '--include-untracked',
  'lint-staged automatic backup'
] +87ms
  lint-staged:git Running git command [ 'stash', 'list' ] +286ms
  lint-staged:git Running git command [ 'stash', 'apply', '--index', 'stash@{0}' ] +114ms
  lint-staged:git Running git command [ 'clean', '-df' ] +454ms
  lint-staged:git Running git command [ 'checkout', '.' ] +90ms
  lint-staged:git Running git command [ 'stash', 'list' ] +433ms
  lint-staged:git Running git command [
  'diff',
  '--unified=0',
  '--no-color',
  '--no-ext-diff',
  '--patch',
  'stash@{0}',
  '-R'
] +143ms
  lint-staged:git Done backing up original state! +2s
Preparing... [completed]
Running tasks... [started]
Running tasks for {stories,src}/**/*.scss [started]
Running tasks for {stories,src}/**/*.{ts,tsx,js} [started]
Running tasks for {stories,src}/**/*.scss [skipped]
→ No staged files match {stories,src}/**/*.scss
  lint-staged:make-cmd-tasks Creating listr tasks for commands 'prettier --write' +0ms
  lint-staged:task cmd: prettier --write C:/Users/Kunduin/Documents/GitHub/vue-space/src/components/VsButton/index.tsx +0ms
  lint-staged:task execaOptions: { preferLocal: true, reject: false, shell: false } +1ms
prettier --write [started]
prettier --write [completed]
Running tasks for {stories,src}/**/*.{ts,tsx,js} [completed]
Running tasks... [completed]
Applying modifications... [started]
  lint-staged:git Running git command [ 'ls-files', '--modified' ] +636ms
  lint-staged:git Restoring unstaged changes... +703ms
  lint-staged:git Running git command [ 'apply', '-v', '--whitespace=nowarn', '--recount', '--unidiff-zero' ] +181ms
  lint-staged:git Done restoring unstaged changes! +179ms
  lint-staged:git Restoring untracked files... +2ms
  lint-staged:file Writing buffer to file `C:/Users/Kunduin/Documents/GitHub/vue-space/.storybook/tsconfig.json` +3s
  lint-staged:file Writing buffer to file `C:/Users/Kunduin/Documents/GitHub/vue-space/src/components/VsInput/index.tsx` +1ms
  lint-staged:file Done writing buffer to file `C:/Users/Kunduin/Documents/GitHub/vue-space/src/components/VsInput/index.tsx`! +3ms
  lint-staged:file Done writing buffer to file `C:/Users/Kunduin/Documents/GitHub/vue-space/.storybook/tsconfig.json`! +1ms
  lint-staged:git Done restoring untracked files! +5ms
Applying modifications... [completed]
Cleaning up... [started]
  lint-staged:git Dropping backup stash... +1ms
  lint-staged:git Running git command [ 'stash', 'list' ] +187ms
  lint-staged:git Running git command [ 'stash', 'drop', '--quiet', 'stash@{0}' ] +155ms
  lint-staged:git Done dropping backup stash! +407ms
Cleaning up... [completed]
  lint-staged tasks were executed successfully! +3s