Remove execute permissions from various non-executable files

- source files and Makefiles need never be executable
- scripts are run directly by their interpreters in the
  test suites, so also do not need to be executable
Whitespace cleanup of all Makefiles*

- some of the %.clean rules in the test-suite Makefiles were using a single tab
  as an empty rule, dangerous! I've replaced these with the safer '@exit 0'.