[clangd] Use all inputs to SystemIncludeExtractor in cache key

Instead of passing in a tooling::CompileCommand into system include
extraction, pass a limited set, whose elements are used as keys.

Also fix the issue around accepting `-isysroot=/foo` which isn't a valid
argument (or the directory should be `=/foo` not `/foo`).

Fixes https://github.com/clangd/clangd/issues/1404
Fixes https://github.com/clangd/clangd/issues/1403

This should also unblock https://reviews.llvm.org/D138546

Differential Revision: https://reviews.llvm.org/D146941