autotools: use variables for paths to allow out-of-tree builds.

[t-w]

Basically, it is not possible to build the project outside of the main project directory, meaning: normally, with autotools, it should be possible to do eg.

./bootstrap
mkdir build
cd build
../configure
make
make check

etc.

However, with fixed relative paths in the config, this is not possible.

These modifications fix the problem with building. The problem remains with couple of failing tests which cannot find test data (probably the data should be copied or referenced in different way in tests, there are ways in autotools to address also that; sometimes it can be tricky and depends on organization of test suite).