Cygwin, for those in the dark is a Linux-like environment for Windows. In the words of Pandu Rao it transforms the "primitive Windows environment" into a usable substitute for a Linux environment. But not everybody is impressed with Cygwin though. Doug Schaefer, in a write up, says that there have been a lot of bug reports on Cygwin off late.
Schaefer was trying to get the Firefox Source set up in the CDT on his laptop running on Windows XP. He used Cygwin for the same. Schaefer says that he found getting the build output into CDT so that Scanner Discovery feature can parse it and set up the include paths and symbols for the indexer tricky. Firefox build wrapped all calls to gcc with a wrapper script, which deals with converting paths.
Schaefer says that most of the bugs were due to Cygwin not supporting Windows path names any more. Schaefer says that the original intent of Cygwin's developers was not to mean it to be a Linux emulation environment on Windows--Cygwin predates Linux popularity.
The problem for CDT, says Schaefer is not that CDT is not running under the Cygwin Environment. It deals only with Windows paths so, they need to convert every Cygwin path they see. Further, while generating makefiles for cygwin make, we need to convert Windows paths to Cygwin paths.
Schaefer's answer to this problem is MinGW, "a much more Windows friendly port of the gnu tool chain, as the gnu environment of choice on Windows". However, he feels that it might be an uphill task to beat the popularity and ease of installation of Cygwin.