enable out of source builds

The changes should be GNU-Make / Autotools compatible. On the machines I have access to they enable out of source builds, for instance :

mculpo@nuvolari:~/epfl/swift$ tree -d -L 2
.
├── build
│   ├── doc
│   ├── examples
│   ├── src
│   └── tests
├── install
│   ├── bin
│   ├── include
│   └── lib
└── sources
    ├── autom4te.cache
    ├── doc
    ├── examples
    ├── m4
    ├── src
    ├── tests
    └── theory

It enables having different build configurations pointing at the same source checkout.

examples/Makefile.am

@@ -19,7 +19,7 @@
 MYFLAGS = -DTIMER
 
 # Add the source directory and debug to CFLAGS
-AM_CFLAGS = -I../src $(HDF5_CPPFLAGS)
+AM_CFLAGS = -I$(top_srcdir)/src $(HDF5_CPPFLAGS)
 
 AM_LDFLAGS = $(HDF5_LDFLAGS)