[cland] Dont emit missing newline warnings when building preamble

When building preamble, clangd truncates file contents. This yielded
errnous warnings in some cases.

This patch fixes the issue by turning off no-newline-at-eof warnings whenever
the file has more contents than the preamble.

Fixes https://github.com/clangd/clangd/issues/744.

Differential Revision: https://reviews.llvm.org/D100501