There really are two parts of your question here. The first is whether or not there are tools that can discover dependencies between CIs and the second is whether or not you can represent them. There are indeed deployment frameworks that can discover dependencies such as exist in a WebSphere or other robust application server although that is kinda like using a sledge hammer to open a walnut.
Probably more reasonable is using version control solutions that allow you to model your software in streams. IBM RTC and Accurev would be two products to look at to see a well defined stream based architecture. Your developers should build in the dependency map when they write the code - most likely using an XML file.
The tool which I am looking for is to draw/define dependency between any 2 files within a project, mostly a SCM tool. The 2 files can be design documents, reports or anything.
Regards
L
On Dimensions you can create and establish relationships between any kind of item (file), no matter what type of item it is (docs, resources, code...whatever)
As per Jose
Serena Dimensions allows this - In fact you can define your own "Relationship Names" and allow/disallow them between Item Types.
eg
A "sub-prog" type could be related to a "prog" type using a "Called-by" relationship.
A "Application" type could be related to a "Server" type using a "Installed on" relationship.
But you wouldn't have a "Server" "installed on" a "program" etc
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