Fix config and start scripts to work on Windows/cygwin

Also fix WebInterfaceServer.java to properly check whether path
is absolute on Windows.

Default directory entries in nephele-user.xml and pact-user.xml
are now commented out because java code will load proper default.
Adjusted cygwin path conversion for path lists.
Revert "Adjusted cygwin path conversion for path lists."

This reverts commit 63d30a05fa290661e59d324384c3f0279e97c51e.
Revert "Fix config and start scripts to work on Windows/cygwin"

This reverts commit a452fd48e971fa17423785398015aac887dbb6c0.
Fix config and start scripts to work on Windows/cygwin

Also fix WebInterfaceServer.java to properly check whether path
is absolute on Windows.

Default directory entries in nephele-user.xml and pact-user.xml
are now commented out because java code will load proper default.