General Linux/yum-related question

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I am using FC 5 and still have much to learn about Linux. One issue that
confuses me relates to the "proper" locations of application files. As a
specific example, I am using the latest Eclipse package, Ver 3.1.2. 

However, I am also experimenting with Eclipse on a Windows machine, and
its version is 3.2. So for comparison purposes, I downloaded Eclipse Ver
3.2 to my home directory on my Linux machine. Thus, I now have two
versions of Eclipse on my Linux machine. (Both seem to work correctly
with the corresponding CDT plugins.) Nevertheless, this raises lots of
questions in my mind:

Is this a sane thing to do?
Should I try to relocate the files into more appropriate directories?
Will this mess up yum?

Please note that I am not too concerned with this specific example. The
problem arises every time I build new applications from the original
source files. I am not sure what to do with the created files. Are there
standard procedures to follow? How will this affect yum-related


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