Doesn't fully integrate with autotools build rules

[jart]

Let's say autotools creates a makefile with this rule:

smash_unittest-lol_test.o: src/lol_test.cc
    # blah blah

Because lol_test.cc is listed in smash_unittest_SOURCES. The problem is that disaster tries to make src/lol_test.o which makes with a generic rule that excludes the per program flags from things like smash_unittest_CPPFLAGS.

This must be fixed.