Closed some .xvg files that were being left open

Closed some .xvg files that were being left open

Closed donor properties file in gmx hbond after removing use of
function static file pointer.

Improved naming and scoping of some file pointers in
analyze_clusters().

Added done_ed() as a place to close the essential dynamics output
file. Later, destructor content for ED should go here (or preferably
RAII).

Removed pr_energy() from gmx_cluster since it was never called.

Change-Id: I4c288e924eb81e9e0f87b8e59ee64dacc0708567