Files in /usr/bin

[Buchbinder, Barry (NIH/NIAID) [E]]

As I understand it, </usr/bin> is mounted on </bin>; everything should be in </cygdrive/c/cygwin/bin> and nothing in </cygdrive/c/cygwin/usr/bin>.

Well, the other day I noticed the following (using Windows Explorer):
	C:\cygwin\bin\    	1,636 files
	C:\cygwin\usr\bin\	1,477 files

I then looked at everything that was in both </cygdrive/c/cygwin/usr/bin> and </cygdrive/c/cygwin/bin>.
  - 'ls' showed that everything had identical timestamps and permissions.
  - 'cmp' showed that everything were identical.

The attachment <unique.txt> contains lists of the 12 files that are in </cygdrive/c/cygwin/usr/bin> but not </cygdrive/c/cygwin/bin> and the 171 files in </cygdrive/c/cygwin/bin> but not </cygdrive/c/cygwin/usr/bin>.

I have been installing everything via setup.  I do have some packages from cygports and things that I've compiled OOTB myself, but they should all be in </usr/local/bin>.

I'd really rather have only one copy of each file.  So my main questions are:
  - Is it is safe for me to delete the duplicated files from </usr/bin> and move the unique files from </usr/bin> to </bin>?
  - Is there something else that I should do?

Questions for my education (meaning no answer is expect):
  - Is this normal or common?
  - How does/might the duplication happen?
  - Would emptying </cygdrive/c/cygwin/usr/bin> and reinstalling everything work?  (I'd do the experiment but I'm reluctant.)

cygcheck.out is attached.

Thanks.

- Barry
  Disclaimer: Statements made herein are not made on behalf of NIAID.
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