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
nit: typo ("prgoram")