fix(cli): skip deleted files in --changed and --staged

[tt-a1i]

Summary

Fix --changed and --staged flags throwing "No such file or directory" error when a file has been deleted or renamed in the working directory but the change hasn't been committed yet.

The issue occurs because:

1. git diff --name-only base...HEAD returns files that exist in HEAD
2. If a file is deleted/renamed in the working directory (uncommitted), it no longer exists on disk
3. The CLI tries to read the non-existent file and throws an error

Solution

Filter out files that no longer exist in the working directory before processing them. This is done in get_changed_files and get_staged_files functions using fs.path_exists().

Test plan

Manual testing:

1. git checkout main
2. echo "const a=1" > test.ts
3. git add test.ts && git commit -m "add test.ts"
4. git checkout -b test
5. echo "const a=2" > test.ts
6. git add test.ts && git commit -m "modify test.ts"
7. mv test.ts test2.ts
8. biome check --changed - should no longer throw error

Closes #4952

[changeset-bot]

🦋 Changeset detected

Latest commit: 207af04

The changes in this PR will be included in the next version bump.

This PR includes changesets to release 13 packages

Name	Type
@biomejs/biome	Patch
@biomejs/cli-win32-x64	Patch
@biomejs/cli-win32-arm64	Patch
@biomejs/cli-darwin-x64	Patch
@biomejs/cli-darwin-arm64	Patch
@biomejs/cli-linux-x64	Patch
@biomejs/cli-linux-arm64	Patch
@biomejs/cli-linux-x64-musl	Patch
@biomejs/cli-linux-arm64-musl	Patch
@biomejs/wasm-web	Patch
@biomejs/wasm-bundler	Patch
@biomejs/wasm-nodejs	Patch
@biomejs/backend-jsonrpc	Patch

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📥 Commits

Reviewing files that changed from the base of the PR and between a392c06 and 207af04.

⛔ Files ignored due to path filters (2)

• crates/biome_cli/tests/snapshots/main_commands_lint/should_skip_nonexistent_changed_files.snap is excluded by !**/*.snap and included by **
• crates/biome_cli/tests/snapshots/main_commands_lint/should_skip_nonexistent_staged_files.snap is excluded by !**/*.snap and included by **

📒 Files selected for processing (3)

• .changeset/fix-changed-deleted-file.md (1 hunks)
• crates/biome_cli/src/changed.rs (2 hunks)
• crates/biome_cli/tests/commands/lint.rs (1 hunks)

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