fix transverse size of IO for level 1

[SeverinDiederichs]

Previously, the size of level 1 IO was the full domain multiplied with the refinement ratio. Now it is at least transversely the correct size.
For the longitudinal resizing, the original box offset etc needs to be known. This is currently not the case.

This will be done in another PR.

• Small enough (< few 100s of lines), otherwise it should probably be split into smaller PRs
• Tested (describe the tests in the PR description)
• Runs on GPU (basic: the code compiles and run well with the new module)
• Contains an automated test (checksum and/or comparison with theory)
• Documented: all elements (classes and their members, functions, namespaces, etc.) are documented
• Constified (All that can be const is const)
• Code is clean (no unwanted comments, )
• Style and code conventions are respected at the bottom of https://github.com/Hi-PACE/hipace
• Proper label and GitHub project, if applicable

[SeverinDiederichs]

Remove deprecated comments

[MaxThevenet]

Looks good, thanks for this PR!