Add an entry to your .profile to set the path to what you want it to be in cygwin.
In cygwin, run the command:
$ <favourite text editor eg vi> ~/.profile
Then set the PATH environment variable to what you want, for example:
export PATH=/cygdrive/c/cygwin/bin
NOTE. I cannot remember if you can use the c: ... version of the path, but if you issue the env command, you will see what it should be.
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