Cygwin has two ROOT tree strcutures and the old one is not the default anymore.

[Donat-Pierre Luigi]

I have two root directory structures (both with usr, bin, etc, ...).  One 
under the standard C:\cygwin ( i.e. /cygdrive/c/cygwin) and the other under 
C:\cygwin\download (i.e.  /cygdrive/c/cygwin/download).
When I enquire about the default bin location here is the reply:
$ which ls
/usr/bin/ls

Here is what leads to it.  The last couple of days I had a problem with 
several DLLs (linintl-1.dll, cygwin DLL, Â…) when I was trying to install new 
components.  At the same time, ls and most command stopped working on a bash 
shell, except few like cd and pwd.  Although it seemed slightly better when 
I redefined the default path to the bin directory with 
PATH="/usr/local/bin:/usr/bin:/bin:$PATH", ls on /usr/bin directory prompted 
more complaints on missing dlls.  It felt as if a lot of the env parameter 
where not defined and cygwin totally incapacitated.

I re-installed the libraries which were reported missing, even though there 
were present in their respective directory.   Out of frustration I 
re-installed the entire base Cygwin and most of the libraries and dev 
components.

Now, everything seems working except that I have two directory structures, 
and the libraries and source code I compiled are in the depreciated 
structure.

Did I break my cygwin?  Can I salvage my old structure in order to save all 
that I had organized and compiled in it (lots of hours)?

Many thanks in advance for your help and suggestions,
Donat-Pierre

P.s.:  I attached a cygcheck.out file for further details (i.e. generated 
with cygcheck -s -v –r ).

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