I think the problem is you are using the wrong algorithm to solve your 
problem.

DFS (depth-first-search) algorithms will easily repeat sequences across 
subtrees.

Starting at CTAgentHome:
CTAgentHome.h and CTAgentHomeRep.h both share the same [FWMOBase.h, 
MOSAgentBasicInfo.h, MOSAgentCriteriaInfo.h, 
MOSAgentInfo.hMOSAgentMessageInfo.h] subtrees.

By the time you're back processing CTAgentHomeRep.h at level aaa, none 
of those class_name's previously seen exist on the stack anymore, so the 
new recursive path doesn't know that they've already been logged.

Or I really don't grok your code, and I haven't had nearly enough coffee 
today.
-- 
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