Avoid using relative paths to include headers

We can use AM_CPPFLAGS to enable global preprocessor options, which can
remove the need for including headers with relative paths.

This commit adds the relevant -I options to AM_CPPFLAGS, and removes all
relative paths to source file headers.

In the future, if we need more control over preprocessor options, we can
add other _CPPFLAGS entries for individual libraries/binaries.