Some pre-commit hooks are incompatible

[ZanSara]

Problem Following several report, we disabled end-of-file-fixer, trailing-whitespace and pretty-format-json from the pre-commit hook's checks.

• end-of-file-fixer and trailing-whitespace seems to conflict with the API generation
• pretty-format-json conflicts with the JSON schema generation They both need further investigation on why they conflict with each other, and how can we resolve that conflict.

Related Work:

• #2929
• https://github.com/deepset-ai/haystack/pull/2903#issuecomment-1199144894
• https://github.com/deepset-ai/haystack/pull/2910#issuecomment-1199204754