gdb/testsuite: Remove duplicates from gdb.base/set-cfd.exp

When running the testsuite, I have:

    Running .../gdb/testsuite/gdb.base/set-cwd.exp ...
    DUPLICATE: gdb.base/set-cwd.exp: test_cwd_reset: continue to breakpoint: break-here

Fix by moving the tests after the 'runto_main' within the same
with_test_prefix scope.

While at it, I fix some indentation issues.

Tested on x86_64-linux.