- Re-fix directory handling

Fix libgcrypt compil under cygwin. It doesn't have gettimeoftheday() and it's wongly detected, so force it. (from markfm 's debugging and googling)

Some sanity checks

Rename flac demux plugin to flacsys

Fix typo of [17361]

Closes #758

- Fix file descriptor leak when opening an empty file
- Don't close STDIN.

(of course, it was obvious reverting the earlier fix would break it,
 but some people don't seem to care about the build system as long as
 "their" feature works).
Oh, and don't let version.c twice in CLEANFILES.