1. is there is any other solution for this issue, instead of replacing the jars inside smartfox? The issue can happen in any kind of jar, and not only this one.
What is exactly the jar you've problems with?
2. Another question is, what would you suggest is the right way for using Spring inside an extension?
I would suggest to avoid Spring
It's a library for very hefyy projects with a large team of devs, tons of dependencies, complex build processes... I don't know, SFS2X Extensions rarely fall into this category. Imho, don't try to crack a nut with a bulldozer.
Unfortunately we don't have suggestions for Spring. I have rarely seen anyone using it in this context, not even the largest projects that run on 50+ SFS instances.
3. Another question about the class loader is: will it add XML files to the class path or only jars? currently it looks to us that only jar work
In terms of accessing files the classpath points to the SFS2X/ folder so you can use that as a point of reference to build your relative paths.
If you mean loading XML files from within a JAR file, that won't work.
Hope it helps