[PB-5623]: fix/fix failing tests

[jzunigax2]

Fixes multiple test failures by addressing API timeout handling, empty file support, and file download issues.

Empty file handling

• Return fs.ErrorCantUploadEmptyFiles when backend doesn't support empty files
• Fixes VFS writeback tests that expect proper error handling

Timeout/conflict recovery

• A bit of an edge case but added defensive recovery from HTTP/2 timeout errors
• Check if file/folder exists after timeout using existence check API
• Treat as success if operation completed server-side despite client timeout
• Prevents 409 conflicts on retry when operation already succeeded

File reading bug fix

• Set o.id = meta.FileID after upload to enable file downloads
• Fixes "File id is malformed" 400 errors when reading uploaded files

Retry logic improvements

• Wrap folder/file operations with pacer for consistent retry behavior
• Handle 401 Unauthorized errors with retry
• Add conflict detection for folder creation (409 → find existing)

Other fixes

• Add EncodeCrLf to default encoder

Test Results

• Before: 5 failing test suites
• After: 1 test with known limitation (empty files not supported by API)
• Fixed: fs/sync, backend/internxt, cmd/bisync, cmd/gitannex, fs/operations, VFS file reading

Note: simulateEmptyFiles should probably be removed in an upcoming refactor PR, I am yet to asses the implications of empty file handling