So here is what I have found so far.

To correct for the hundreds of thousands of TheadLocal entries I just needed to 
do CRS. cleanupThreadLocals() at the end each request to my service.

The case of the eternal instances of ObliqueStereographic and 
ObliqueOrthographic is because the pool of CRSPair's in 
BufferedCoordinateOperationFactory is just caching way too much, at least for 
my needs and slowing down everything as time goes by.  For a simple test I 
disabled the use of the pool and I was able to go beyond 25000 maps providing a 
consistent response time of 1.2 sec to my callers; when the pool was enabled my 
response time was 19.7 sec at the same point, which was unacceptable for my 
requirements.

Now, maybe this is just my bad.  I should have used cleanupThreadLocals() from 
the beginning but ... well ... I'm learning.

I wonder if there is a way to use an alternative to 
BufferedCoordinateOperationFactory.  I noticed there is a 
DefaultCoordinateOperationFactory, which is not using the pool and may be the 
one I need ... the question is how do I enable that one?

Obviously I am new in GeoTools.

Thanks in advance for any suggestions of recommendations.

-Felipe


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