|The Glasgow Haskell Compiler User's Guide, Version 6.2|
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The cygwin tools aim to provide a unix-style API on top of the windows libraries, to facilitate ports of unix software to windows. To this end, they introduce a unix-style directory hierarchy under some root directory (typically / is C:\cygwin\). Moreover, everything built against the cygwin API (including the cygwin tools and programs compiled with cygwin's ghc) will see / as the root of their file system, happily pretending to work in a typical unix environment, and finding things like /bin and /usr/include without ever explicitly bothering with their actual location on the windows system (probably C:\cygwin\bin and C:\cygwin\usr\include).
GHC, by default, no longer depends on cygwin, but is a native windows program. It is built using mingw, and it uses mingw's ghc while compiling your Haskell sources (even if you call it from cygwin's bash), but what matters here is that - just like any other normal windows program - neither GHC nor the executables it produces are aware of cygwin's pretended unix hierarchy. GHC will happily accept either '/' or '\' as path separators, but it won't know where to find /home/joe/Main.hs or /bin/bash or the like. This causes all kinds of fun when GHC is used from within cygwin's bash, or in make-sessions running under cygwin.
Don't use absolute paths in make, configure & co if there is any chance that those might be passed to GHC (or to GHC-compiled programs). Relative paths are fine because cygwin tools are happy with them and GHC accepts '/' as path-separator. And relative paths don't depend on where cygwin's root directory is located, or on which partition or network drive your source tree happens to reside, as long as you 'cd' there first.
If you have to use absolute paths (beware of the innocent-looking ROOT=`pwd` in makefile hierarchies or configure scripts), cygwin provides a tool called cygpath that can convert cygwin's unix-style paths to their actual windows-style counterparts. Many cygwin tools actually accept absolute windows-style paths (remember, though, that you either need to escape '\' or convert '\' to '/'), so you should be fine just using those everywhere. If you need to use tools that do some kind of path-mangling that depends on unix-style paths (one fun example is trying to interpret ':' as a separator in path lists..), you can still try to convert paths using cygpath just before they are passed to GHC and friends.
If you don't have cygpath, you probably don't have cygwin and hence no problems with it... unless you want to write one build process for several platforms. Again, relative paths are your friend, but if you have to use absolute paths, and don't want to use different tools on different platforms, you can simply write a short Haskell program to print the current directory (thanks to George Russell for this idea): compiled with GHC, this will give you the view of the file system that GHC depends on (which will differ depending on whether GHC is compiled with cygwin's gcc or mingw's gcc or on a real unix system..) - that little program can also deal with escaping '\' in paths. Apart from the banner and the startup time, something like this would also do:
$ echo "Directory.getCurrentDirectory >>= putStrLn . init . tail . show " | ghci