configure: Order AC_OUTPUT more logically

Start with Makefiles before alphabetically listed files/subdirs, e.g:

      Makefile
      local-gen
      a/Makefile
      a/b/Makefile
      c/Makefile
      c/a/Makefile
Add a scripts/ subdirectory

Issue #114.
scripts: Add a git/ subdir

Issue #114.
scripts: Add a git/hooks subdir

Issue #114.
configure: Export AM_CONDITIONALS as substrings
scripts/git: Add a pre-commit hook

Issue #114.
scripts/git: Install git hooks into git directory

Issue #115.
configure: Add an --enable-git-hooks argument

Issue #115.
build/scripts/git: Only install git hooks with enabled

Issue #115.