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I'm getting this same problem even though I'm using a different version identifier name in my project (MySQLDocs) instead of D_Ddoc.
The problem appears to be compiler-related. Using ddox v0.16.12, I get this problem on DMD 2.078.0 and up. But on DMD 2.077.1 and below it works fine, with no duplicate entries. I don't know if DMD 2.078.0 introduced a bug, or if maybe it just made a change to its json doc output that ddox isn't aware of.
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