automake cleanup: moving files, renaming inttypes.h

- Created a makefile-env with basic automake init.
- In "includes", inttypes.h was cluttering the system's one. This caused
  random build errors on some systems/in some conditions. Renaming it.
- Moved some tools from src to src/tools.
- Moved some tests from src to src/test.
- More various makefile cleanups.

Signed-off-by: Roald J. van Loon <roaldvanloon@gmail.com>