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I would like to write a shell script to automate the doxygen by taking input folders automatically by identifying that which folder has doxygen supported file types.

Can anybody please help me on the possible ways of doing it ?

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You don't have to use shell script here,as the documention goes:

doxygen -g <config-file>

this will create a configurable file for your needs,and for more information please refer to the link.And also refer to another post: https://stackoverflow.com/questions/51667/best-tips-for-documenting-code-using-doxygen

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