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I was looking for a some kind of app (other than ant migration tool) that could analyze a code base pulled from a Salesforce org and show all dependencies between the files (for example – between apex classes and visualforce pages).

The only thing that I've figured out so far – is to rename apex classes to have .java extension – and then to use IntelliJ IDEA to build a UML diagram for those files. It worked great for showing dependencies between different apex classes, but it does not show whether any of the class methods are used by any visualforce page. And grep-ing all the time does not seem like a great plan.

Any suggestions on a tool, or, at least, a common practice to find out all the dependencies between different metadata files?

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There are a number of tools outlined in Apex static code analysis, although most of them are online. In particular the post by Robert Sösemann on the static code analyzer that integrates with Eclipse.

Another option would be to extract the SymbolTables in addition to the Metadata files. This will give you the dependencies that Salesforce has derived on last compile.

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I don't think any such tool exist as of now specifically for salesforce. The spectrum of salesforce offline tools is very limited. Also note that this kind of information can be easily found on salesforce interface. Because of that offline tools are not in demand. Due to these reasons neither private companies nor community groups are interested in working on such tool.

If this something you must have then you would need to write custom plugin for this.

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