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Ensure configure.h is always 1st. included header.
Maybe we could eventually introduce gcc -include option, but for now
this better uses dependency tracking.
Also move _REENTRANT and _GNU_SOURCE into configure.h so it
doesn't need to be present in various source files.
This ensures consistent compilation of headers like stdio.h since
it may produce different declaration.
As we start refactoring the code to break dependencies (see doc/refactoring.txt),
I want us to use full paths in the includes (eg, #include "base/data-struct/list.h").
This makes it more obvious when we're breaking abstraction boundaries, eg, including a file in
metadata/ from base/
