> I'm a novice in mod_perl but I already surprised with its features !

Before you continue any further with new questions it's a time to read 
the guide: http://perl.apache.org/guide/

> Could you please help me with following two things:
> 
> 1) What is the most common directory structure for mod_perl
> web-applications ?
> I keep all my modules in a separate directory (which is closed for
> internet-users) and I have to add path to them to @INC (for automatic
> reloading).
> But what if
> there are several applications with modules of the same name (like
> config.pm or utils.pm) ?


You have to fully qualify these. E.g. MyProject1::config, 
MyProject2::config and etc. You will find more examples in the guide.

 
> 2) Suppose I want to share variable $q between several modules.


http://perl.apache.org/guide/perl.html#Using_Global_Variables_and_Shari

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