Doesn't fully integrate with autotools build rules

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.