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.
Merge pull request #60 from aljoscha/master

Cygwin Fix Again