Environment information

CLI:
  Version:                      1.5.0
  Color support:                true

Platform:
  CPU Architecture:             x86_64
  OS:                           linux

Environment:
  BIOME_LOG_DIR:                unset
  NO_COLOR:                     unset
  TERM:                         "xterm-256color"
  JS_RUNTIME_VERSION:           "v21.5.0"
  JS_RUNTIME_NAME:              "node"
  NODE_PACKAGE_MANAGER:         "pnpm/8.14.0"

Biome Configuration:
  Status:                       Loaded successfully
  Formatter disabled:           false
  Linter disabled:              false
  Organize imports disabled:    false
  VCS disabled:                 false

Workspace:
  Open Documents:               0

What happened?

If a file is deleted at commit time, biome check and biome ci using the --changed option will recognize the deleted file as a check target, resulting in a read error for a file that does not actually exist.

Step to reproduce

1. Delete the file and commit on a branch different from the vcs.defaultBranch setting.

2. Run biome check --changed .
   Output:

   eslint.config.js internalError/io  INTERNAL  ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
   
     ✖ No such file or directory (os error 2)
     
     ⚠ This diagnostic was derived from an internal Biome error. Potential bug, please report it if necessary.
   

Additional info

This problem was discovered during the creation of a CI process using Biome.
(RShirohara/unified-webnovel#227)

Expected result

If the --changed option is used, deleted files are expected to simply be ignored.

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